RetrogeneDB ID: | retro_cjac_4181 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:65737308..65738026(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C11orf84 | ||
| Ensembl ID: | ENSCJAG00000018418 | ||
| Aliases: | None | ||
| Description: | chromosome 11 open reading frame 84 [Source:HGNC Symbol;Acc:25115] |
Retrocopy-Parental alignment summary:
>retro_cjac_4181
ATGGCCCTAAAGGCTGAGGGCACTGCACCTGACTGCTTGAGGTGATGCTCAAATGTGAGGAAGGGGAGAATGAGAAGGAT
GCCATGGTTGTGGCCCTAATTCCACAGGTTTAGTTGATGTTAAGAGTGACCCAACAAGAGAAGACCTGACTGCCTAGACC
CAGCCCTCTGGAGGTGGGCAGCAATGACTGTGAGGAGCCCAAGCAGCATGTGTCTTGGGACCAGGAGTTTCTGGTGGGCA
GCAGCCCAAGATGAAGTGGGCCTGCACTGTGCATGGTGTGTGGCACTGAGATCCTGGCACCCTCAGCTGACGTGGCTTAC
TAGCACATCCTGGAGCAGCATCCTCACAGTGTGGACTTGAGTCCTTCCAAGAAGAACAACATCCTGGAGACCTGGAGTGA
AGGGGTGGCTCTCTTGCAAGACGTCAGAGCTGAGCAGTCGTCCACACCCAACTCAGACTCAGGCCAGGATGCCCAACTAG
ACCCAGACTCTAACCCAGACTCTGGCAGAATGCCAGCTGAAATTGTCATTCTCCTGGACTCTGAGAATAACCCATCCCTC
CCTTAAAGGAGCCAACCCAGGGGATTCTGTCTCCTCAAGCTTCTTGCTGCCCTTGCCACAGAGCCAGGAAATAAGAAGCC
CTGTGGTCAGAGATGGAAGCCCCCAGGGGGCGAGGAAGCCAGAAAGAAAAGAGGCAGACCATGACCAAAGACCTGGAC
ORF - retro_cjac_4181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.84 % |
| Parental protein coverage: | 63.25 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVKAEGAALDCF-EVTLKCEEGEDEEEAMVGPYSARPEPMLRVTQQEKTPPPRSSPLEAGSDSCEEPKQ |
| MA.KAEG.A.DC..EV.LKCEEGE.E..AMV.........MLRVTQQEKT..PR.SPLE.GS..CEEPKQ | |
| Retrocopy | MALKAEGTAPDCL<EVMLKCEEGENEKDAMVVALIPQV*LMLRVTQQEKT*LPRPSPLEVGSNDCEEPKQ |
| Parental | QVSWEQEFLVGSSPGGSGRALCMVCGAEIRAPSADTARSHILEQHPHTLDLSPSEKSNILEAWSEGVALL |
| .VSW.QEFLVGSSP..SG.ALCMVCG.EI.APSAD.A..HILEQHPH..DLSPS.K.NILE.WSEGVALL | |
| Retrocopy | HVSWDQEFLVGSSPR*SGPALCMVCGTEILAPSADVAY*HILEQHPHSVDLSPSKKNNILETWSEGVALL |
| Parental | QDIRAEQPSPPHSDSGQDAHPDPDSNPDPARVPAEIVVLLDSEDNPSLPKRSRPRGLRPLELPAVPATEP |
| QD.RAEQ.S.P.SDSGQDA..DPDSNPD..R.PAEIV.LLDSE.NPSLP.RS.PRG...L.L.A..ATEP | |
| Retrocopy | QDVRAEQSSTPNSDSGQDAQLDPDSNPDSGRMPAEIVILLDSENNPSLP*RSQPRGFCLLKLLAALATEP |
| Parental | GNKKPRGQRWKEPAGEEPVRKKRGRP-MTKNLD |
| GNKKP.GQRWK.P.GEE..RKKRGRP.MTK.LD | |
| Retrocopy | GNKKPCGQRWKPPGGEE-ARKKRGRP<MTKDLD |
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 .42 RPM | 0 .58 RPM |
| SRP051959_heart | 1 .28 RPM | 1 .88 RPM |
| SRP051959_kidney | 0 .87 RPM | 0 .98 RPM |
| SRP051959_liver | 0 .56 RPM | 0 .71 RPM |
| SRP051959_lung | 1 .33 RPM | 3 .46 RPM |
| SRP051959_lymph_node | 0 .37 RPM | 4 .41 RPM |
| SRP051959_skeletal_muscle | 0 .50 RPM | 0 .92 RPM |
| SRP051959_spleen | 0 .99 RPM | 1 .68 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4181 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4181 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4181 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000015053 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000018418 | 1 retrocopy |
retro_cjac_4181 ,
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