RetrogeneDB ID: | retro_cjac_865 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:83392187..83393531(+) | ||
| Located in intron of: | ENSCJAG00000006739 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GALNT1 | ||
| Ensembl ID: | ENSCJAG00000021030 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_865
ATGAGAAAATTTGCATACTGAAAGATGGTCCTAGCCACCTCCTTGATTTGGGTACTCTTGGATATGTTCCTGCTGCTTTA
CTTCAGTAAATGCAACAAATGTGATGAAAAAAAGGAGAAAGGATTTCCTGCTGGGGATATTCTAGAGCCAGTACAAAAAC
CTCATGAAGGTCCTGGAGAAATGGGAAAACCAGTCATAATCCCTAAAGAGGATCAAGAAAAGTTGAAAGAGATCTTTAAA
ATCATTCAATTCAATTTAATCGCAAGTGAAATGATTGCACTCAACAGATCTTTATCAGATGTTAGGTTAGAAGAGTGTAA
AACAAAGGTATATCCAGGTATTCTTCCTACAAGTGTGGTGATTGTTTTCTGCAATAAGGCTTGGAGCACACTTCTGCCAA
CTGTCTATAGTGTCATTAATTGCTCACCAAGAAACTGGATGGAAGAAATTGTTCTAGTAAATGATGGCAGTGAAAGAGAC
TTTTTGAAAAGGATTTTAGAGAGTTATGTGAAAAAACTAAGAGTACCAGTTCATATAATTCAAATGGAACAACGTTTTGG
ATGGATCAGAGCTAGATTAAAAGGAGCTGCTCTGTCTACAGACCAAGTGATCACCTTCCTGGATGCTCATTGTGAGTGTA
CAGTGGGGTGGCTGAAGCCTTTCTTGGCCAGGATCAAACATGACAGGAGAACAGTGGTGTGTCCTATCATCAATGTGATC
AGCGATGATACTTTTGAGTACATAGCAGGCTCTGATATGACTTATGGTAGGTTCAAGTGGAAGCTCAATTTTTGCTGGTA
TCCTGTTCCCCAGAGAGAAATGGGCAGAAGGAAAGGTGATCGGACACTTCGCATTAGAACACCTACCATGGCAGAAGGCC
TTTTTTCAATAGACAGAGATTACTTTCAGGAAATGGGAACATATGATGCTGAAAAGGATATCTGGGGAGGAGAAAACCTA
GAAATTTCCTTTCAGATTTGACAGTGTGGAGGAACTTTGGAAACTGTTACATGCTCACATGTTAGACATGTGTTTCAAAA
AGCTACAACTTACACATTTCCAGGAGGCACAGGGCAGATTATCAATAAAAATAATAGACAATTTGCAGAAGTGTGGATGG
ATGAATTCAAGAATTTCTTCTATATAATTTCTCCAGATGTTACAACGGCAGATTATGGAGCTATATCATCAAGAGCTGGT
CTAAGACACAAACTACAATGCAAACCTTTTTCTTGGTACTTAGAGAATATTTATCCTGATTCTCAAATTCCATGTCACTA
TTTCTCATTGGGAGAGATGAGAAGTGTGGAAATAAATCAGTGTCTAGATAACATAGCTAGAAAA
ORF - retro_cjac_865 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.67 % |
| Parental protein coverage: | 80.36 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEKKERGLPAGDVLEPVQKPHEGPGEMGKPVVIPKE |
| MRKFAY.K.VLATSLIWVLLDMFLLLYFS.CNKCDEKKE.G.PAGD.LEPVQKPHEGPGEMGKPV.IPKE | |
| Retrocopy | MRKFAY*KMVLATSLIWVLLDMFLLLYFSKCNKCDEKKEKGFPAGDILEPVQKPHEGPGEMGKPVIIPKE |
| Parental | DQEKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVI |
| DQEK.KE.FKI.QFNL.ASEMIALNRSL.DVRLE.CKTKVYP..LPT.SVVIVF.N.AWSTLL.TV.SVI | |
| Retrocopy | DQEKLKEIFKIIQFNLIASEMIALNRSLSDVRLEECKTKVYPGILPT-SVVIVFCNKAWSTLLPTVYSVI |
| Parental | NRSPRHMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDA |
| N.SPR...EEIVLV.D.SERDFLKR.LESYVKKL.VPVH.I.MEQR.G.IRARLKGAA.S..QVITFLDA | |
| Retrocopy | NCSPRNWMEEIVLVNDGSERDFLKRILESYVKKLRVPVHIIQMEQRFGWIRARLKGAALSTDQVITFLDA |
| Parental | HCECTVGWLEPLLARIKHDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKG |
| HCECTVGWL.P.LARIKHDR.TVVCPII.VISDDTFEY.AGSDMTYG.F.WKLNF.WYPVPQREM.RRKG | |
| Retrocopy | HCECTVGWLKPFLARIKHDRRTVVCPIINVISDDTFEYIAGSDMTYGRFKWKLNFCWYPVPQREMGRRKG |
| Parental | DRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT |
| DRTL..RTPTMA.GLFSIDRDYFQE.GTYDA..DIWGGENLEISF.I.QCGGTLE.VTCSHV.HVF.KAT | |
| Retrocopy | DRTLRIRTPTMAEGLFSIDRDYFQEMGTYDAEKDIWGGENLEISFQI*QCGGTLETVTCSHVRHVFQKAT |
| Parental | PYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPAGVTKVDYGDISSRVGLRHKLQCKPFSWYLENIY |
| .YTFPGGTGQIINKNNR..AEVWMDEFKNFFYIISP..VT..DYG.ISSR.GLRHKLQCKPFSWYLENIY | |
| Retrocopy | TYTFPGGTGQIINKNNRQFAEVWMDEFKNFFYIISP-DVTTADYGAISSRAGLRHKLQCKPFSWYLENIY |
| Parental | PDSQIPRHYFSLGEIRNVETNQCLDNMARK |
| PDSQIP.HYFSLGE.R.VE.NQCLDN.ARK | |
| Retrocopy | PDSQIPCHYFSLGEMRSVEINQCLDNIARK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .02 RPM | 61 .30 RPM |
| SRP051959_heart | 0 .05 RPM | 37 .08 RPM |
| SRP051959_kidney | 0 .00 RPM | 44 .57 RPM |
| SRP051959_liver | 0 .02 RPM | 37 .06 RPM |
| SRP051959_lung | 0 .03 RPM | 54 .30 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 67 .94 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 39 .83 RPM |
| SRP051959_spleen | 0 .02 RPM | 54 .05 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_865 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_865 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_865 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000011206 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000021030 | 2 retrocopies |
retro_cjac_1554, retro_cjac_865 ,
|
| Myotis lucifugus | ENSMLUG00000001978 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000000420 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000003311 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000014610 | 1 retrocopy |