RetrogeneDB ID: | retro_cjac_1357 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:82595339..82596558(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM214B | ||
| Ensembl ID: | ENSCJAG00000009210 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 214, member B [Source:HGNC Symbol;Acc:25666] |
Retrocopy-Parental alignment summary:
>retro_cjac_1357
AGTGCCACCTCTTCTTGGATTTCAGGGGCCTGGAGTCCCTCCTGGCCGCCATCATATGCTTCCTGCAATACTTTGCACAA
CAGAGACCAGGCTTTCCCAGAACCAGGGGACAAGGGTCCCTGGGGCAGTCCCCAGAGCCAGCCCTCTGGACCAGCTGCAC
ACACTTGACACTGATTTGCACAGTCTTGCACAAATGAGGGGTAAGAGCCCAGTGGCTAGGGTGGGCAATGGGGGAGCCTC
TGGCCTAGGGGAGTCCCCAAGCACTGCCAGTGGGCATGGTCTCAAGCACACACCCCCAGCCCTGGATCTCCAGGCCCCTG
CCCCACCAAGAGAAGGCTGCTTCCTGCTGGAGAAGCCCCAGATGTCAGCTCTGAGGAAGAGGAGCCACCCTTTGGAGGTG
CCAGGGAACCCTGGGCTACCCTACTGCTACTAACTGTTCTGATGCCCAAACCACACCCTCTGGAGACACCTTGCTGTCTG
GGCCCAAGAAGCACAGTTTCAGACCCAACAGACTGCATTCCCATGGGGCGGAGGCTGAGAGGTGCCTGTTGCCTAGAGCT
GGGCCCACTTCAAAGCCTCTGGAAGGGGCCAGGCCTGCTGAGTCTCCCCAGTGCCTCCCCTGTTCCTCCCCCTGCTGTCA
GTTGCACCCTGCGGGGCAACTTTGAGGATTTGTTGCTGCAAGGATGCTTTGCACCATCTGGCCACATTAAGGGCTTCACA
GCAGAGACTGGAGCTAGTGGGTCCTACTGCGTCCAGCATGTCACACTACCTGTCACCATCACCTTCTTTGAGGTTTCTGA
GCAAAATGCCCCCAACCCCACTGGGCCTTATGGAGCCGAACACCCTGGGGAGGAAGACTCACAGTGTGTCCAAAGTGGGC
ACCATCCAAATGACATTATTTAACCCCAACCAGACTGTGGTGAAGATGTTCCTGGTAATCTTTGACTTCTTGGGCATGGC
TGCTGCCCACATGCCCTTCCTGTGCAATCACCTCTTTTTGGTGCCTGTGGGTGAGGAGGAAAACGCTAACTCCACCCACT
GCCTTCTCTGCTATTCTCTGCACCTGAGGTTCCAGAACTCCCACTTAGGCCTCTTAAGCCTGAATAGAGATCTCCACCTG
CTTTTTTCCCACTAGAGCCTGGAGCTGGACACAGGGCTTCCCTACGAACTGCAGGCTGTAACTGAGGCCCCTCCTAATCC
ACGTTATTAGCCTTTGCCC
ORF - retro_cjac_1357 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.84 % |
| Parental protein coverage: | 75.84 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | SVTSSWTSGAWSPPCPPSNASCNTLHTRDWASPDPG-GQGSLGASPGPA-PPGQLHTIDTDLHSLAQIGG |
| S.TSSW.SGAWSP..PPS.ASCNTLH.RD.A.P.PG.GQGSLG.SP.PA.P..QLHT.DTDLHSLAQ..G | |
| Retrocopy | SATSSWISGAWSPSWPPSYASCNTLHNRDQAFPEPG<GQGSLGQSPEPA<PLDQLHTLDTDLHSLAQMRG |
| Parental | KSPVAGVGNGR-SLWPR-ESPGTANGHSPEHTPPG-PGPPGPCPTKRRLLPAGEAPDINSEEE-GPAPRR |
| KSPVA.VGNG..SLWPR.ESP.TA.GH...HTPP..PG.PGPCPTKRRLLPAGEAPD..SEEE.G....R | |
| Retrocopy | KSPVARVGNGG<SLWPR>ESPSTASGHGLKHTPPA<PGSPGPCPTKRRLLPAGEAPDVSSEEE<GATLWR |
| Parental | RRGTLGHPTAANSSDAKATPFWSHLLPGPKE-PVLDPTDCSPMGRRLKGARRLKLSPLRNLRKGPGLLSA |
| ..GTLG.PTA.N.SDA..TP....LL.GPK...V.DPTDC.PMGRRL.GA..L.L.PL..L.KGPGLLS. | |
| Retrocopy | CQGTLGYPTATNCSDAQTTPSGDTLLSGPKK>TVSDPTDCIPMGRRLRGACCLELGPLQSLWKGPGLLSL |
| Parental | PSASPVPTPAVSRTLLGNFEESLLRERFAPSGHIEGFTAEIGASGSYCPQHVTLPVTVTFFDVSEQNA-P |
| PSASPVP.PAVS.TL.GNFE..LL...FAPSGHI.GFTAE.GASGSYC.QHVTLPVT.TFF.VSEQNA.P | |
| Retrocopy | PSASPVPPPAVSCTLRGNFEDLLLQGCFAPSGHIKGFTAETGASGSYCVQHVTLPVTITFFEVSEQNA>P |
| Parental | APFLGVMDLKPLGRKGYSVPKVGTIQVTLFNPNQTVVKMFLVTFDFSDMPAAHMTFLRHRLFLVPVGEEG |
| .P.LG.M....LGRK..SV.KVGTIQ.TLFNPNQTVVKMFLV.FDF..M.AAHM.FL...LFLVPVGEE. | |
| Retrocopy | TP-LGLMEPNTLGRKTHSVSKVGTIQMTLFNPNQTVVKMFLVIFDFLGMAAAHMPFLCNHLFLVPVGEEE |
| Parental | NANPTHRLLCYLLHLRFRSSRSGRLSLHGDIRLLFSRRSLELDTGLPYELQAVTEAPHNPRYSPLP |
| NAN.TH.LLCY.LHLRF..S..G.LSL..D..LLFS..SLELDTGLPYELQAVTEAP.NPRY.PLP | |
| Retrocopy | NANSTHCLLCYSLHLRFQNSHLGLLSLNRDLHLLFSH*SLELDTGLPYELQAVTEAPPNPRY*PLP |
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 .04 RPM | 10 .89 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .95 RPM |
| SRP051959_kidney | 0 .00 RPM | 5 .24 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .82 RPM |
| SRP051959_lung | 0 .03 RPM | 9 .58 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 3 .47 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .55 RPM |
| SRP051959_spleen | 0 .02 RPM | 7 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1357 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1357 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1357 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000009210 | 1 retrocopy |
retro_cjac_1357 ,
|
| Homo sapiens | ENSG00000005238 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000003218 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000005528 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000011862 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000004530 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000019101 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000020904 | 1 retrocopy |