RetrogeneDB ID: | retro_cjac_2424 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:31965473..31966667(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000032895 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ERI2 | ||
| Ensembl ID: | ENSCJAG00000009400 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2424
GCAACCAAGCAGCTGGCGCAGCAGCTTGGATTAATTAGGAGAAAGTCAGTTGCATCAGCAAATGGGAACCTAGGAAGAAG
CAAATCCAAGCAGTTGCTTGACTACTTAATTGTCATTGATTTTGAATCGACATGCTGGAATGATGGGAAATGCCACCATA
GCCGGGAAGTAACTGAATTTCCAGCAGTGTTGCTGAACACATCAACTGGACAGATTGAGTCTGAGTTCAGTGCTTATGTT
CAACCTCAGGAACATCCCGTTCTTTCAGAATTTTGCATGGAATTGACAGGCATAAAGCAGGCTCAAGTTGATGAAGGAGT
CCCTCTGAAGATTTGCTTATCTCAGTTCTGTAAATGGATTCATAAGATTCAGCAACAGAAGAAGAACCTTATTTTTGCTG
CTGGGGTTTCAGAGCCTTCTACTTCTGAAGTAAACGCTTATACATTTGTTACGTGGTCAGACTGGGACTTGGGGGTGTGA
CTGGAGTATGAGTGTAAAAGAAAGCAGTTGTTAAAACCAGTGTTTTTAAATTCTTGGATTGATCTCAGAGAAACTTACAA
GCTTTTCTATAGGAGAAAACCAGAAGGACTAAGTGGTGCCTTGCAGGAAGGGGGAATAGAATTCTCAGGACGAGATCATT
CTGGGTTGGACGATTCTCAGAATACTGCCCTTCTTGCTTGGAAAATGGTCAGGGATGGCTGTCTAGTGAAAATTACAAGG
TCGTTGAACAAGGTTCCCACTAAGAAGAATTCCAGCATTCTGGCCAGAAATTTGGATACAAATCAAGTTGAAGAAATGTC
TGCCTGTAACAGCATCCGGGGTCCTAGCATCTATAATAAGGAGCCTAAAAAATACAATAAATTCTATGAAAAAGTTCAAA
TGAAGTCAGTTTGTGCAAATTTTCCTATAAAGGCACAGAAGGATCAATTACAAGTAAAGAACAATATAAAAACAGGTCTT
CACAATGTCAAAAGTTGCTTATCTATTATTAATTCTAAGCCCTCTACTTCTCTGGGGCATTTGCAGTCTCCTACCTTGAA
TTCACCTATCTACATGCAAAAGCAAGGAAAAAATGAACATCTTGCTTTTAATACCAAATCTAAGTCTTCAACAGTTGGTT
CAGAATTGGTGCTTGTTTCTACCAGCATTCTGACTGTTAATCATGTTTCTGATATGGAAATGAGCTCTACTCTT
ORF - retro_cjac_2424 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.75 % |
| Parental protein coverage: | 57.64 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ATKRLARQLGLIRRKSIASANGNLGRSKSKQLFDYLIVIDFESTCWNDGKRHHSQEIIEFPAVLLNTSTG |
| ATK.LA.QLGLIRRKS.ASANGNLGRSKSKQL.DYLIVIDFESTCWNDGK.HHS.E..EFPAVLLNTSTG | |
| Retrocopy | ATKQLAQQLGLIRRKSVASANGNLGRSKSKQLLDYLIVIDFESTCWNDGKCHHSREVTEFPAVLLNTSTG |
| Parental | QIESEFHAYVQPQEHPILSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQK-NIIFAAGVSEPS |
| QIESEF.AYVQPQEHP.LSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQK.N.IFAAGVSEPS | |
| Retrocopy | QIESEFSAYVQPQEHPVLSEFCMELTGIKQAQVDEGVPLKICLSQFCKWIHKIQQQKKNLIFAAGVSEPS |
| Parental | TSEVNLCAFVTWSDWDLGVCLEYECKRKQLLKPVFLNSWIDLRATYKLFYRRKPKGLSGALQEVGIEFSG |
| TSEVN...FVTWSDWDLGV.LEYECKRKQLLKPVFLNSWIDLR.TYKLFYRRKP.GLSGALQE.GIEFSG | |
| Retrocopy | TSEVNAYTFVTWSDWDLGV*LEYECKRKQLLKPVFLNSWIDLRETYKLFYRRKPEGLSGALQEGGIEFSG |
| Parental | REHSGLDDSRNTALLAWKMIKDGCLMKITRSLNKVPTKKNSSILARNLNTNQVEEMSACNSIQGPSIYN- |
| R.HSGLDDS.NTALLAWKM..DGCL.KITRSLNKVPTKKNSSILARNL.TNQVEEMSACNSI.GPSIYN. | |
| Retrocopy | RDHSGLDDSQNTALLAWKMVRDGCLVKITRSLNKVPTKKNSSILARNLDTNQVEEMSACNSIRGPSIYNK |
| Parental | EP-KNTINS-HVKVQMKSVCANFPIKAQKDQLQVKNNIKTSLHNVKSCLSIINSKSSTSLGHLQSPTLNS |
| EP.KNTINS...KVQMKSVCANFPIKAQKDQLQVKNNIKT.LHNVKSCLSIINSK.STSLGHLQSPTLNS | |
| Retrocopy | EP>KNTINS<YEKVQMKSVCANFPIKAQKDQLQVKNNIKTGLHNVKSCLSIINSKPSTSLGHLQSPTLNS |
| Parental | PIYMQKQGKNEHLAFNTKCESSTVGSELVLVSTTIPTVNHVSDMEMSSTL |
| PIYMQKQGKNEHLAFNTK..SSTVGSELVLVST.I.TVNHVSDMEMSSTL | |
| Retrocopy | PIYMQKQGKNEHLAFNTKSKSSTVGSELVLVSTSILTVNHVSDMEMSSTL |
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 | 4 .02 RPM |
| SRP051959_heart | 0 .04 RPM | 3 .03 RPM |
| SRP051959_kidney | 0 .07 RPM | 6 .41 RPM |
| SRP051959_liver | 0 .02 RPM | 6 .11 RPM |
| SRP051959_lung | 0 .03 RPM | 1 .87 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .51 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .01 RPM |
| SRP051959_spleen | 0 .08 RPM | 2 .27 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2424 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2424 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2424 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003995 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000009400 | 1 retrocopy |
retro_cjac_2424 ,
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