RetrogeneDB ID: | retro_cjac_2409 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:13697753..13698952(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000021566 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2409
CTGCAGCGGAAGATGGAGAACCGTGATTACCGGGATGCACAGGAGTTTCCTGCTGACGTACGGCTTATGTTCTCTAACTG
CTATAAGTACAACCCCCCAGATCACGATGTTGTGGCAATGGCACAAAAGCTACAGGACATATTTGACTTCCGTTATGCCA
AGATGCCAGATGAACCACTGGAACCAGGGCCTTTACCAGTCTCTACTGCCACATGCCCCCTGGCTGGCCCAAATTATCTT
CAGAGTCCTCCAGTGAGGAAAGTAGCAGTGAGAGCTCCTCTGAGGAAGAGGAGGAGGAAGATGAGGAGGACGAGGAACAA
GAAGAGAGTGAAAGCTCAGACCCAGACGAAGAAAGGGCTCATCGCTTGACAGTACACAGGGACAGCTTCGGGCAGTACAT
GAACAACTGGCTGCTCTGTCCCAGGGTCCAATATCCAAGCCCAAGAGGAAAAGAGAGAAAAAGAAGAAACAGAAGGCAGA
GAAGCACGGAGGACGAGCTGGGGTTGATGAAGATGACAAGGGGCCTTGAGCACCCCTGCCCACCTCAGCCCAAGAAGTCC
AGGAAAGCAAGTGGCAATGGAGGTGGCAGTGCTGCTTTAGGCCCTTCTGGCTTTGGACCTTCTGGAGGAAGTGGCACCAA
GCTCCCCAAAAAGGCCACAAAGACAGCCCCACCTGCCCTGCCAACAGGTCATGATTCAGAGGAGGAGGAAGAGAGCAGGC
CCAAGAGTTAGGATGAAAAGCGGCAGCTGGGCCTGGACATTAACAAATAACCTGGAGAGAAGCTGGGCCAACTTGTGCAC
ATAATCCAAGCCAGGGAACCCTCTTTACATGATTCAAACCCAGAAGAGATTGAGATTGATTTTGAAACACTCAAGCCATC
CACACTCAGAGAGCTTGAGCGCTATGTCCTTTCCTGCCTATGTAAGAAACCTCACAAGCCCTACACCATTAAGGAGGCTG
TGGGAAAGACAAAGGAAGAACTGGCTTTGGAGAAAAAGTGGGAATTAGAAAAGCAGTTACAAGATGTCAGCGGACAGCTC
AATTCCACTAAAAAGCCCCCCAAGAAAGCGAGTGAGAAAACAGAGTCATCCTCTGCACAGCAAGTAATAGTGTCACACCT
TAGTGCTTCCAGCTCCAGCTCAGATTCCAGCTCCTCCTCTTCGTCATCTTTTTCAGACACCAGTGATTCAGACTCAGGC
ORF - retro_cjac_2409 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.84 % |
| Parental protein coverage: | 59.12 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPDEPLEPGPLPVSTA |
| ..RKMENRDYRDAQEF.ADVRLMFSNCYKYNPPDHDVVAMA.KLQD.F.FRYAKMPDEPLEPGPLPVSTA | |
| Retrocopy | LQRKMENRDYRDAQEFPADVRLMFSNCYKYNPPDHDVVAMAQKLQDIFDFRYAKMPDEPLEPGPLPVSTA |
| Parental | IPPGLAKSSSES-SSEE-SSSESSSEEEEEEDEEDEE-EESESSDSEEERAHRLA-ELQEQLRAVHEQLA |
| ..P........S.SS.E.SSSESSS..........EE.EESESSD..EERAHRL....Q.QLRAVHEQLA | |
| Retrocopy | TCPLAGPNYLQS<SSSEESSSESSSXXXXXXXXXXEEQEESESSDPDEERAHRLT<STQGQLRAVHEQLA |
| Parental | ALSQGPISKPKRKREKKEKKKKRKAEKHRGRAGADEDDKGPRAPR-PPQPKKSKKASVSGGGSAALGPSG |
| ALSQGPISKPKRKREKK...KK.KAEKH.GRAG.DEDDKGP.AP..PPQPKKS.KAS..GGGSA...... | |
| Retrocopy | ALSQGPISKPKRKREKK---KKQKAEKHGGRAGVDEDDKGP*APL>PPQPKKSRKASGNGGGSAXXXXXX |
| Parental | FGPSGGSGTKLPKKATKTAPPALPTGYDSEEEEESRPMSYDEKRQLSLDINKLPGEKLGRVVHIIQAREP |
| .....GSGTKLPKKATKTAPPALPTG.DSEEEEESRP.S.DEKRQL.LDINK.PGEKLG..VHIIQAREP | |
| Retrocopy | XXXXXGSGTKLPKKATKTAPPALPTGHDSEEEEESRPKS*DEKRQLGLDINK*PGEKLGQLVHIIQAREP |
| Parental | SLRDSNPEEIEIDFETLKPSTLRELERYVLSCLRKKPRKPYTIKKPVGKTKEELALEKKRELEKRLQDVS |
| SL.DSNPEEIEIDFETLKPSTLRELERYVLSCL.KKP.KPYTIK..VGKTKEELALEKK.ELEK.LQDVS | |
| Retrocopy | SLHDSNPEEIEIDFETLKPSTLRELERYVLSCLCKKPHKPYTIKEAVGKTKEELALEKKWELEKQLQDVS |
| Parental | GQLNSTKKPPKKASEKTESSSAQQVVVSRLSASSSSSDSSSSSSSSSSSDTSDSDSG |
| GQLNSTKKPPKKASEKTESSSAQQV.VS.LSASSSSSD.SSSSSSSS.SDTSDSDSG | |
| Retrocopy | GQLNSTKKPPKKASEKTESSSAQQVIVSHLSASSSSSD-SSSSSSSSFSDTSDSDSG |
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 .00 RPM | 53 .38 RPM |
| SRP051959_heart | 0 .00 RPM | 53 .22 RPM |
| SRP051959_kidney | 0 .02 RPM | 73 .99 RPM |
| SRP051959_liver | 0 .00 RPM | 46 .18 RPM |
| SRP051959_lung | 0 .00 RPM | 81 .14 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 77 .87 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 37 .74 RPM |
| SRP051959_spleen | 0 .00 RPM | 74 .96 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2409 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2409 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2409 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000021566 | 2 retrocopies |
retro_cjac_2409 , retro_cjac_564,
|
| Oryctolagus cuniculus | ENSOCUG00000003097 | 1 retrocopy |