RetrogeneDB ID: | retro_cjac_2773 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:138648542..138650060(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XRCC1 | ||
| Ensembl ID: | ENSCJAG00000013552 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2773
ACCTCATCCCTCTGGCCAAGTGAAGCCCACGAAATTGACATGCCGGAGATCCGCTTCTGCCATGTAGTGTCCTACAGCAG
CCAGGACTCAACCCACTGTGCAGAAAATCTTCTCAAGGCAGACACTTACTGAAAATGACGGGCAGCCAAGGTAGGTGAGA
AGACCATCTCTGTGGTCCTACAGTTGGAGAAGGAGGAACAGATACACAGTGGGCACGTCGGGAATGATGGCTCAGCTTTC
GTGGAGGTGCTAGTGGTCAGCTCGGCTGGAGGTGCTGAGGAGCAAGACTATGAGGTCCTTCTGGTCACCTCATCTTTCAT
GTCCCCTTCTGAGAGTCGCAGTGGTTCAAACCCCAACCGCGTTCGCATGTTTGGGCCTAAAAAGCTGGTCCGGGCAGCAG
CCGAGAAGTGCTGGGACCGGGTCAAAATTCTTTGCAGCCAGCCCTACAGCAAGGACTCCCCCTTTGACCTGAGTTTTGTA
CGGTGTCATAGCCCTCCAGACAAAGATGAGGCAGAGGCCCCGTCCCAGAAGGTGATCGTGACCAAGCTCAGCCAGTTCCA
TGTGAAGGAGGAGGACTAGAGGGCCAACTCCCTGAGGCCGGGGGCTGTCTTCTTCAGCAGGGTCAAAAAGACATCCCCAG
CCACAGCCAGGGACCTGGCAGGACCCAGCTACGCAGCTGCCACCCTCCAGGCCTCCAGTGCTGCCTCCTCAGCCTCTCCA
GTCTCCACGGCTGTAGGCAGCACCTTCGAGCCCCAGGAGTCTCCCAAAGGGAAGAGGAAGTTGGATTTGAACCAAGAAGA
AAAGAAGACCCCCAGCAAACCACCACCCCAGCTGTCGCCACCGGTTTCCAAGAGACCTAAATTGCCAGCTCCCACCGGTA
CCCCAGCCACAGCCCCAGTCCCTGTCCCAGCACAGGGGGTGGTGACAGGCCAGCCCCGAGGAGAAGGAACCCAGCCCAGA
CGATCACGAGCTGGCCCAGAGGAGCTGGGGAAGATGCTTCAGGGTGTGGTAGTGGTGCCGAGTGGCTTCCAGAACCCCTT
CTGCTCTGAACTGCGAGATAAGGCCCTAGAGCTGGGGGCCAAGTATCGGCCAGACTGGACCCCAGACAGCACGCACCTCA
TCTGTGCCTTTGTGAACACCCCCAAGTACAGCCAGGTCCCAGGCCTCGGAGGCCGCATCGTGCATACGGAGTGGGTGCTG
GACTGTCACCGCATTCGTCGGCGGCTGCCCTCCCGGAGGTACCTCATGGCAGGGCCAGACTGGAGCAGTGAGGACAATGA
GGCCTCTCACAGTGGTGGCAGTGGTGATGAAGCCCCCAAGCTTCCTCGAAAGTATCCCCAGATCAAAACCAAGCTCACTC
AGGCAGCTGGACCCAGCTCACCCCAGAAGCCCCCAACCCCAGAAGAGACCAAAGCAGCCTCACCAGTGCCCCAGGAAGAT
ACAGACATTGAGGGGGAACAGTCAGAAGGACAGGACAATGGGGCAGAAAATTCTGGGGACACAGAAGATGAGCTGAGA
ORF - retro_cjac_2773 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.57 % |
| Parental protein coverage: | 77.11 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TSSLWPSEAHEIDMPEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHS |
| TSSLWPSEAHEIDMPEIR..HVVS.SSQDSTHCAENLLKADTY.K.RAAK.GEKTISVVLQLEKEEQIHS | |
| Retrocopy | TSSLWPSEAHEIDMPEIRFCHVVSYSSQDSTHCAENLLKADTY*K*RAAKVGEKTISVVLQLEKEEQIHS |
| Parental | VDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDR |
| ...GNDGSAFVEVLV.SSAGGA.EQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGP.KLVRAAAEK.WDR | |
| Retrocopy | GHVGNDGSAFVEVLVVSSAGGAEEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPKKLVRAAAEKCWDR |
| Parental | VKIVCSQPYSKDSPFGLSFVRFHSPPDKDEAEAPSQKVTVTKLGQFRVKEEDESANSLRPGALFFSRVKK |
| VKI.CSQPYSKDSPF.LSFVR.HSPPDKDEAEAPSQKV.VTKL.QF.VKEED..ANSLRPGA.FFSRVKK | |
| Retrocopy | VKILCSQPYSKDSPFDLSFVRCHSPPDKDEAEAPSQKVIVTKLSQFHVKEED*RANSLRPGAVFFSRVKK |
| Parental | TSQATASDVAGPSYAAATLQASSAASSASPVSRAIGSTSKLQESP--KGKRKLDLNQEE---KKTPSKPP |
| TS.ATA.D.AGPSYAAATLQASSAASSASPVS.A.GST...QESP..K.K..L.........K..P...P | |
| Retrocopy | TSPATARDLAGPSYAAATLQASSAASSASPVSTAVGSTFEPQESPKGKRKLDLNQEEKKTPSKPPPQLSP |
| Parental | PQLLPPVSKRPKCKSVVLTESILHP-QGVVTGQPRGEGTEPRRSRAGPEELGKILQGVVVVLSGFQNPFR |
| P....P..K.P.......T.....P.QGVVTGQPRGEGT.PRRSRAGPEELGK.LQGVVVV.SGFQNPF. | |
| Retrocopy | PVSKRP--KLPAPTGTPATAPVPVPAQGVVTGQPRGEGTQPRRSRAGPEELGKMLQGVVVVPSGFQNPFC |
| Parental | SELRDKALELGAKYRPDWTPDSTHLICAFANTPKYSQVLGLGGRIVRKEWVLDCHRMRRRLPSRRN-VAG |
| SELRDKALELGAKYRPDWTPDSTHLICAF.NTPKYSQV.GLGGRIV..EWVLDCHR.RRRLPSRR...AG | |
| Retrocopy | SELRDKALELGAKYRPDWTPDSTHLICAFVNTPKYSQVPGLGGRIVHTEWVLDCHRIRRRLPSRRYLMAG |
| Parental | AGGLQMRVEGSHAGASGTEEPDFYKKRKPQTKTKPTQAAGPSSPQKPPTPEETKAASPVPQEDRDIEGEQ |
| ........E.SH.G.SG.E.P....K..PQ.KTK.TQAAGPSSPQKPPTPEETKAASPVPQED.DIEGEQ | |
| Retrocopy | PDWSSEDNEASHSGGSGDEAPKLPRK-YPQIKTKLTQAAGPSSPQKPPTPEETKAASPVPQEDTDIEGEQ |
| Parental | SEGQDNGAEDSGDTEDELR |
| SEGQDNGAE.SGDTEDELR | |
| Retrocopy | SEGQDNGAENSGDTEDELR |
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 .11 RPM | 6 .57 RPM |
| SRP051959_heart | 0 .12 RPM | 8 .52 RPM |
| SRP051959_kidney | 0 .33 RPM | 12 .29 RPM |
| SRP051959_liver | 0 .04 RPM | 4 .81 RPM |
| SRP051959_lung | 0 .36 RPM | 11 .78 RPM |
| SRP051959_lymph_node | 0 .30 RPM | 14 .41 RPM |
| SRP051959_skeletal_muscle | 0 .17 RPM | 4 .96 RPM |
| SRP051959_spleen | 0 .29 RPM | 12 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2773 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2773 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2773 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013552 | 1 retrocopy |
retro_cjac_2773 ,
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