Characterization of genomic location of transcriptionally activated provirus
| CLGY number . | Genomic position relatively to nearest transcript . | Chromosome . | Nearest gene . | Ortholog prediction of nearest gene to human (if not noted otherwise) . |
|---|---|---|---|---|
| 1 | Donor splice site, intron 1. | 9 | p110 | Dead-box protein 3 (DDX3X) |
| 2 | nd4 | nd | — | — |
| 3 | 395 bp downstream | 23 | Novel prediction | her4 |
| 4§ | 5649 bp downstream | 16 | Apoeb | Apolipoprotein A-I precursor (APOA1) |
| 5§ | 2nd intron | 7 | Pax6b | Paired box protein PAX-6 (PAX6) |
| 6¶ | 4727 bp upstream | 5 | Tbx16 | T-box transcription factor TBX6 (TBX6) |
| 7 | nd4 | nd | — | — |
| 8¶ | In exon | 16 | Genscan prediction | nd |
| 9 | 2692 bp upstream | 20 | Novel prediction | NHS-like 1 (NHSL1) |
| 10 | nd2 | nd | — | — |
| 11§ | 32,296 bp upstream. | 1 | Otx1I | nd |
| 12 | 814 bp downstream | Zv4 NA6752 | Novel prediction | Chromosome 10 open reading frame 104 (C10orf104) |
| 14 | nd4 | nd | — | — |
| 16 | 1st intron | 15 | Hsp47 | Serpin I2 precursor (SERPINI2) |
| 18 | 1st intron | 16 | Genscan prediction | Odd Oz/ten-m homolog 3 (ODZ3) |
| 19 | 7470 bp upstream | 22 | Novel prediction | ATP synth. delta chain, mitochondrial prec. (ATP5D) |
| 20§ | 1360 bp upstream | 18 | Rara2a | Retinoic acid receptor beta (RARB) |
| 21§ | 14,041 bp downstream | 11 | Snai1a | Zinc finger protein SLUG (SNAI2) |
| 22§ | 70,441 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 24§ | 3153 bp upstream | 16 | Pou5f1 | POU domain, class 5, transcription factor 1 (POU5F1) |
| 30 | nd2 | Zv4 NA16664 | — | — |
| 31 | 1st intron | 20 | Zgc:56602 | Hypothetical protein FLJ11712 |
| 32§ | 6th intron | 22 | Genscan prediction | nd |
| 33 | nd4 | 9 | Genscan prediction 00000003859 | Smad-interacting protein1b |
| 35*,¶ | 8084 bp upstream | 16 | Pou5f1 | POU domain, class 5, transcription factor 1 (POU5F1) |
| 38 | 10th intron | 22 | Novel prediction | RAB GTPase activating protein 1 (RABGAP1) |
| 39 | 36,022 bp downstream | 19 | Novel prediction | Similar to CG6405 gene product (NM_145269). |
| 41§ | 5890bp upstream | 22 | Novel prediction | Transducin-like enhancer protein 1 (TLE1) |
| 47§ | 1st intron | 3 | Novel prediction | Glucose-6-phosphatase (G6PC) |
| 50 | 1st intron | Zv4 NA12687 | Genscan prediction | nd |
| 65§ | 132,831 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 68 | 4th intron | Zv4 NA17998 | Genscan prediction | nd |
| 69¶ | 3′UTR | Zv4 scaffold335 | Hoxa9a | Homeobox protein HOX-A9 (HOXA9) |
| 75†,§ | 14 027 bp downstream | 5 | Sox19 | Transcription factor SOX-19 (SOX19) |
| 77 | 884 bp upstream | 18 | Gro2 | Transducin-like enhancer protein 3 (TLE3) |
| 86 | 69,259 bp upstream | 14 | Novel prediction | Potential phospholipid transporting ATPase IG (ATP11C) |
| 97 | 5th intron | 6 | Novel prediction | Probable urocanate hydratase (HUTU_HUMAN) |
| 101 | 10,487 bp downstream | 13 | Q804r3 | ORF2 of novel retrotransposon. |
| 102§ | 2nd intron | 2 | Novel prediction | nd |
| 104 | nd4 | nd | — | — |
| 109 | nd1 | nd | — | — |
| 128‡,§ | 257 bp down-/2634bp upstream | 8 | Novel/foxd4 | COBW-like protein (NM_018491)/Forkhead box D4 |
| 129 | nd4 | nd | — | — |
| 130 | 2nd intron | 1 | Efnb2b | Ephrin-B2 precursor (EFNB2) |
| 131§ | 2675 bp upstream | 24 | Ccnd1 | G1/S-specific cyclin D1 (CCND1) |
| 135 | nd4 | nd | — | — |
| 142 | nd4 | nd | — | — |
| 143 | nd4 | nd | — | — |
| 151 | 2335 bp upstream | 10 | Tpbgl | Trophoblast glycoprotein (TPBG) |
| 154 | nd2 | 13 | — | — |
| 155 | nd1 | nd | — | — |
| 158 | nd1 | nd | — | — |
| 159 | nd4 | nd | — | — |
| 160 | nd1 | nd | — | — |
| 162§ | 3001 bp downstream | 16 | Apoeb | Apolipoprotein A-I precursor (APOA1) |
| 182 | nd4 | nd | — | — |
| 183 | 2899 bp downstream | 14 | Emx3 | nd |
| 185§ | 4902 bp upstream | 23 | Hoxc8a | Homeobox protein HOX-C8 (HOXC8) |
| 186 | 2208/4635 bp downstream4 | 14 | Genscan prediction | Zinc finger protein 36, C3H type-like 1 (ZFP36L1) |
| 188 | nd1 | nd | — | — |
| 189 | 57,383 bp downstream | 9 | Zgc:55421 | Protein tyrosine phosphatase like (PTPLB) |
| 195 | nd2 | Zv4 NA3586 | — | — |
| 196§ | 5th intron | 4 | Genscan prediction | SRY-family |
| 197 | nd2 | Zv4 NA13949 | — | — |
| 198§ | 3988 bp upstream | 23 | Hoxc8a | Homeobox protein HOX-C8 (HOXC8) |
| 202§ | 2nd intron | 24 | Novel prediction | Mitogen-activated protein kinase 3 (MAP3K3) |
| 205§ | 222,949 bp upstream | 20 | Sox11b | sox11 |
| 215 | 1st intron | 5 | Genscan prediction | nd |
| 229 | 22,927 bp upstream | nd | Fgfr1 | Fibroblast growth factor receptor 1 (FGFR1) |
| 232 | 1st intron | 4 | Zgc:55542 | Protein phosphatase 1, regulatory subunit 3B (PPP1R3B) |
| 236 | 5th intron | 22 | Novel prediction | nd |
| 237§ | 3970 bp upstream | 4 | Myf5 | Myogenic factor MYF-5 (MYF5) |
| 238§ | 73 bp downstream | 12 | Hoxb1b | Homeobox protein HOX-B1 (HOXB1) |
| 239§ | 4th intron | 5 | Zgc:55984 | Branched-chain a-ketoacid dehydrogenase kin (BCKD) |
| 258 | nd1 | nd | — | — |
| 263 | 175 bp upstream | 20 | Novel prediction | Mediator of DNA damage checkpoint 1 (MDC1) |
| 264§ | 5th intron | 20 | Novel prediction | P-selection precursor (SELP) |
| 266 | nd4 | nd | — | — |
| 268 | nd1 | nd | — | — |
| 287§ | 4th intron | 11 | Novel prediction | nd |
| 298§ | 4906 bp downstream | 4 | Ube2h | Ubiquitin conjugating enzyme E2H (UBE2H) |
| 299 | nd1 | nd | — | — |
| 308 | nd1 | nd | — | — |
| 318§ | 1st intron | 10 | Cldn7 | Claudin-7 (CLDN7) |
| 368§ | 89,331 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 369§ | 2nd intron | 10 | Zgc:77101 | Ubiquitin-like 3 (Ubl3) |
| 372§ | 743 bp upstream | 24 | Ccnd1 | G1/S-specific cyclin D1 (CCND1) |
| 373 | nd1 | nd | — | — |
| 375¶ | 348 bp upstream | 2 | Ptc1 | Patched protein homolog 1 (PTCH) |
| 376§ | 74,656 bp downstream | 21 | Novel prediction | Double-stranded RNA-binding zinc finger protein 346 (NM_012279) |
| 379 | 3rd intron | 9 | Genscan prediction | Adenylate cyclase 6, isoform a (ADCY6) |
| 381 | nd2 | Zv4 NA14257 | — | — |
| 383§ | 2651 bp downstream | 20 | Genscan prediction | nd |
| 391 | nd4 | nd | — | — |
| 393 | 5th intron | 20 | Novel prediction | Gamma-tubulin complex component 2 (TUBGCP2) |
| CLGY number . | Genomic position relatively to nearest transcript . | Chromosome . | Nearest gene . | Ortholog prediction of nearest gene to human (if not noted otherwise) . |
|---|---|---|---|---|
| 1 | Donor splice site, intron 1. | 9 | p110 | Dead-box protein 3 (DDX3X) |
| 2 | nd4 | nd | — | — |
| 3 | 395 bp downstream | 23 | Novel prediction | her4 |
| 4§ | 5649 bp downstream | 16 | Apoeb | Apolipoprotein A-I precursor (APOA1) |
| 5§ | 2nd intron | 7 | Pax6b | Paired box protein PAX-6 (PAX6) |
| 6¶ | 4727 bp upstream | 5 | Tbx16 | T-box transcription factor TBX6 (TBX6) |
| 7 | nd4 | nd | — | — |
| 8¶ | In exon | 16 | Genscan prediction | nd |
| 9 | 2692 bp upstream | 20 | Novel prediction | NHS-like 1 (NHSL1) |
| 10 | nd2 | nd | — | — |
| 11§ | 32,296 bp upstream. | 1 | Otx1I | nd |
| 12 | 814 bp downstream | Zv4 NA6752 | Novel prediction | Chromosome 10 open reading frame 104 (C10orf104) |
| 14 | nd4 | nd | — | — |
| 16 | 1st intron | 15 | Hsp47 | Serpin I2 precursor (SERPINI2) |
| 18 | 1st intron | 16 | Genscan prediction | Odd Oz/ten-m homolog 3 (ODZ3) |
| 19 | 7470 bp upstream | 22 | Novel prediction | ATP synth. delta chain, mitochondrial prec. (ATP5D) |
| 20§ | 1360 bp upstream | 18 | Rara2a | Retinoic acid receptor beta (RARB) |
| 21§ | 14,041 bp downstream | 11 | Snai1a | Zinc finger protein SLUG (SNAI2) |
| 22§ | 70,441 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 24§ | 3153 bp upstream | 16 | Pou5f1 | POU domain, class 5, transcription factor 1 (POU5F1) |
| 30 | nd2 | Zv4 NA16664 | — | — |
| 31 | 1st intron | 20 | Zgc:56602 | Hypothetical protein FLJ11712 |
| 32§ | 6th intron | 22 | Genscan prediction | nd |
| 33 | nd4 | 9 | Genscan prediction 00000003859 | Smad-interacting protein1b |
| 35*,¶ | 8084 bp upstream | 16 | Pou5f1 | POU domain, class 5, transcription factor 1 (POU5F1) |
| 38 | 10th intron | 22 | Novel prediction | RAB GTPase activating protein 1 (RABGAP1) |
| 39 | 36,022 bp downstream | 19 | Novel prediction | Similar to CG6405 gene product (NM_145269). |
| 41§ | 5890bp upstream | 22 | Novel prediction | Transducin-like enhancer protein 1 (TLE1) |
| 47§ | 1st intron | 3 | Novel prediction | Glucose-6-phosphatase (G6PC) |
| 50 | 1st intron | Zv4 NA12687 | Genscan prediction | nd |
| 65§ | 132,831 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 68 | 4th intron | Zv4 NA17998 | Genscan prediction | nd |
| 69¶ | 3′UTR | Zv4 scaffold335 | Hoxa9a | Homeobox protein HOX-A9 (HOXA9) |
| 75†,§ | 14 027 bp downstream | 5 | Sox19 | Transcription factor SOX-19 (SOX19) |
| 77 | 884 bp upstream | 18 | Gro2 | Transducin-like enhancer protein 3 (TLE3) |
| 86 | 69,259 bp upstream | 14 | Novel prediction | Potential phospholipid transporting ATPase IG (ATP11C) |
| 97 | 5th intron | 6 | Novel prediction | Probable urocanate hydratase (HUTU_HUMAN) |
| 101 | 10,487 bp downstream | 13 | Q804r3 | ORF2 of novel retrotransposon. |
| 102§ | 2nd intron | 2 | Novel prediction | nd |
| 104 | nd4 | nd | — | — |
| 109 | nd1 | nd | — | — |
| 128‡,§ | 257 bp down-/2634bp upstream | 8 | Novel/foxd4 | COBW-like protein (NM_018491)/Forkhead box D4 |
| 129 | nd4 | nd | — | — |
| 130 | 2nd intron | 1 | Efnb2b | Ephrin-B2 precursor (EFNB2) |
| 131§ | 2675 bp upstream | 24 | Ccnd1 | G1/S-specific cyclin D1 (CCND1) |
| 135 | nd4 | nd | — | — |
| 142 | nd4 | nd | — | — |
| 143 | nd4 | nd | — | — |
| 151 | 2335 bp upstream | 10 | Tpbgl | Trophoblast glycoprotein (TPBG) |
| 154 | nd2 | 13 | — | — |
| 155 | nd1 | nd | — | — |
| 158 | nd1 | nd | — | — |
| 159 | nd4 | nd | — | — |
| 160 | nd1 | nd | — | — |
| 162§ | 3001 bp downstream | 16 | Apoeb | Apolipoprotein A-I precursor (APOA1) |
| 182 | nd4 | nd | — | — |
| 183 | 2899 bp downstream | 14 | Emx3 | nd |
| 185§ | 4902 bp upstream | 23 | Hoxc8a | Homeobox protein HOX-C8 (HOXC8) |
| 186 | 2208/4635 bp downstream4 | 14 | Genscan prediction | Zinc finger protein 36, C3H type-like 1 (ZFP36L1) |
| 188 | nd1 | nd | — | — |
| 189 | 57,383 bp downstream | 9 | Zgc:55421 | Protein tyrosine phosphatase like (PTPLB) |
| 195 | nd2 | Zv4 NA3586 | — | — |
| 196§ | 5th intron | 4 | Genscan prediction | SRY-family |
| 197 | nd2 | Zv4 NA13949 | — | — |
| 198§ | 3988 bp upstream | 23 | Hoxc8a | Homeobox protein HOX-C8 (HOXC8) |
| 202§ | 2nd intron | 24 | Novel prediction | Mitogen-activated protein kinase 3 (MAP3K3) |
| 205§ | 222,949 bp upstream | 20 | Sox11b | sox11 |
| 215 | 1st intron | 5 | Genscan prediction | nd |
| 229 | 22,927 bp upstream | nd | Fgfr1 | Fibroblast growth factor receptor 1 (FGFR1) |
| 232 | 1st intron | 4 | Zgc:55542 | Protein phosphatase 1, regulatory subunit 3B (PPP1R3B) |
| 236 | 5th intron | 22 | Novel prediction | nd |
| 237§ | 3970 bp upstream | 4 | Myf5 | Myogenic factor MYF-5 (MYF5) |
| 238§ | 73 bp downstream | 12 | Hoxb1b | Homeobox protein HOX-B1 (HOXB1) |
| 239§ | 4th intron | 5 | Zgc:55984 | Branched-chain a-ketoacid dehydrogenase kin (BCKD) |
| 258 | nd1 | nd | — | — |
| 263 | 175 bp upstream | 20 | Novel prediction | Mediator of DNA damage checkpoint 1 (MDC1) |
| 264§ | 5th intron | 20 | Novel prediction | P-selection precursor (SELP) |
| 266 | nd4 | nd | — | — |
| 268 | nd1 | nd | — | — |
| 287§ | 4th intron | 11 | Novel prediction | nd |
| 298§ | 4906 bp downstream | 4 | Ube2h | Ubiquitin conjugating enzyme E2H (UBE2H) |
| 299 | nd1 | nd | — | — |
| 308 | nd1 | nd | — | — |
| 318§ | 1st intron | 10 | Cldn7 | Claudin-7 (CLDN7) |
| 368§ | 89,331 bp upstream | 20 | Sox11b | Transcription factor SOX-11 (SOX11) |
| 369§ | 2nd intron | 10 | Zgc:77101 | Ubiquitin-like 3 (Ubl3) |
| 372§ | 743 bp upstream | 24 | Ccnd1 | G1/S-specific cyclin D1 (CCND1) |
| 373 | nd1 | nd | — | — |
| 375¶ | 348 bp upstream | 2 | Ptc1 | Patched protein homolog 1 (PTCH) |
| 376§ | 74,656 bp downstream | 21 | Novel prediction | Double-stranded RNA-binding zinc finger protein 346 (NM_012279) |
| 379 | 3rd intron | 9 | Genscan prediction | Adenylate cyclase 6, isoform a (ADCY6) |
| 381 | nd2 | Zv4 NA14257 | — | — |
| 383§ | 2651 bp downstream | 20 | Genscan prediction | nd |
| 391 | nd4 | nd | — | — |
| 393 | 5th intron | 20 | Novel prediction | Gamma-tubulin complex component 2 (TUBGCP2) |
Flanking sequences of activated proviruses were obtained using LIM-PCR(Wu et al., 2003). Genomic position of the integrated vector was identified by BLASTN of the flanking sequence against the Ensembl zebrafish genome browser (zebrafish whole genome shotgun assembly sequence version 4, Zv4)(http://www.ensembl.org/).
Abbreviations: nd, not determined; nd1, no hits in Zv4 assembly (10); nd2,provirus integrated in non-assembled sequence (6); nd4, multiple hits with at least 95% identity (13).
Genscan predictions are supported by EST data in ENSEMBL.
CLGY35 is closer to a novel gene (6353 bp upstream), but shows the expression pattern of pou5f1.
CLGY75 is closer to a novel gene (11,148 bp upstream), but shows the expression pattern of sox19.
CLGY128 is in between foxd4 and a novel gene, closer to the latter. The expression pattern is consistent with a forkhead domain factor.
Integrations mapped to finished sequence.
Cases in unfinished scaffold sequence that could be confirmed by in situ pattern.