RetrogeneDB ID: | retro_cjac_1507 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:34441368..34442494(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM38 | ||
| Ensembl ID: | ENSCJAG00000010938 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1507
TATAAAATGTCATGTGAGAACATAGAGAACAGATCCACCTGCTCTGCAAAGATGAAGGACAGCTCATCTGCTGGTGCTGT
GAGCAGGCACCGTAACACAAAGGGCACACCACAGTGCTTGTTGAAGACATATGCCAGAGCTACAAGTAAAGCTCCACAAA
GTTGTGACAAATTTGAGGCAACTTGAAGACAGATGTACGGAGCAGAAGCTGTTGACGGCAATACAAATAACTAAATGAAA
GAAAAGATACAGATTCAGAGACAAAAAATTCCAGTCTGACTTTAAGGGTCTCCAGAATTTCCTACAAGAGAAAGAGAAGG
GTTATCTCTGGAGACTGGAAAAAGAATAACAACAGACTCTGAGTAGACTGAGGGACCATGAGGCCAGTCTGAGGCTGAAG
AGTGATTAACTCAAGAGCCATATCCTGGAACTGGAGGAAAAGTTCAGGGCTCAGACCAGAAATTGCTGCAGAATGTAAAT
GACACTTTGAGCAAGAGTTGGGCGGCAAAGCTGGAAACATCAGAGGCCGTCTCCTTGGAGCTTCATACTATGTGCAATGT
TTCTGAGCTTTACTTTGATGTGAAGAAAATGTTAAGGAGTCATCATGTCAGTGTGGTTCTGGATCCAGATACAGCTCATC
ATGAACTAATTCTGTCTGAAGATCAGAGACAAGTGACTCAAGGATACCCCCACTGAATCAGGACACTTCCTCCAGGAGAT
TTAGTTTCTTGCCCTGTGTCTTGGGTTGTGAAGGTTTCACCTCAGGAAGATGCTACTTTGAAGTGCATGTTAGAGAAGGA
ACTGGGTGGATTTAGGAGTTTGTATGCAAAATGTGCAAAGGGGCACTGGCATGAAGCAAGAGCCTCAGTTCCAATTCTGG
ACCCTCAGGCTGTGCAAAAAGAAAGGTTATGTAGCACTTACTTCCCCCCCAACTTCCTTTCATCTGCATGAGTAGCACCT
GGTTGTGAGAGTTTTTCTGGACTATGAGGCCGGAGTTGTATCCTTTTACAATGGGAATACTGGCTGCCACATTTTCACCT
TCCCAAAGGCTTCCTTCTCTGATATTCTCTGGCCCTATTTCCAGGTTTATCATCATTATCCTTTGCTTCTGCCTCCCCTA
GATGAT
ORF - retro_cjac_1507 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.81 % |
| Parental protein coverage: | 81.08 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | HEMSCE-EHREQLHLFCEDEGRLICWRCERAPQHKGHTTVLVEEVCQGYK-EKLQNAVTNLRQLEDRCTE |
| ..MSCE.EHREQ.HL.C.DEG.LICW.CE.AP.HKGHTTVLVE..CQ.YK..KL...VTNLRQLEDRCTE | |
| Retrocopy | YKMSCE<EHREQIHLLCKDEGQLICWCCEQAP*HKGHTTVLVEDICQSYK<VKLHKVVTNLRQLEDRCTE |
| Parental | QKLFTAIQITK-WKEKIQIQRQKI-QSDFKSLQSFLHEEEKCYLWRLEKEEQQTLSRLRDREASLGLKSD |
| QKL.TAIQITK..KEKIQIQRQKI.QSDFK.LQ.FL.E.EK.YLWRLEKE.QQTLSRLRD.EASL.LKSD | |
| Retrocopy | QKLLTAIQITK<MKEKIQIQRQKI>QSDFKGLQNFLQEKEKGYLWRLEKE*QQTLSRLRDHEASLRLKSD |
| Parental | ELNRHILELEEK-CQGSAQKLLQNVNDTLSRSGAVKLETSEAVSLELHTMCNVSELYFDVKKMLRSHQVS |
| .L..HILELEEK..QGS.QKLLQNVNDTLS.S.A.KLETSEAVSLELHTMCNVSELYFDVKKMLRSH.VS | |
| Retrocopy | *LKSHILELEEK<VQGSDQKLLQNVNDTLSKSWAAKLETSEAVSLELHTMCNVSELYFDVKKMLRSHHVS |
| Parental | VTLDPDTAHHELILSEDRRQVTRGYPQ-QNQDTSSRRFSALPCVLGCEGFTSGRCYFEVDVGEGTGW-DL |
| V.LDPDTAHHELILSED.RQVT.GYP...NQDTSSRRFS.LPCVLGCEGFTSGRCYFEV.V.EGTGW.DL | |
| Retrocopy | VVLDPDTAHHELILSEDQRQVTQGYPH<LNQDTSSRRFSFLPCVLGCEGFTSGRCYFEVHVREGTGW<DL |
| Parental | GVCVENVQRGTGMKQEPQFGFWTLRLCKKKGYVALTSPPTSLLLPEQPLVVGVFLDCEAGVVSFYNGTTG |
| GVC..NVQRGTGMKQEPQF.FWTLRLCKKKGYVALTSPPTS..L.E..LVV.VFLD.EAGVVSFYNG.TG | |
| Retrocopy | GVCMQNVQRGTGMKQEPQFQFWTLRLCKKKGYVALTSPPTSFHLHE*HLVVRVFLDYEAGVVSFYNGNTG |
| Parental | CHIFTFPKASFSDTLRPYFQVYHYSPLFLPPLDD |
| CHIFTFPKASFSD.L.PYFQVYH..PL.LPPLDD | |
| Retrocopy | CHIFTFPKASFSDILWPYFQVYHHYPLLLPPLDD |
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 | 10 .10 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .52 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .63 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .74 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .11 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 16 .92 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .71 RPM |
| SRP051959_spleen | 0 .00 RPM | 17 .27 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1507 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1507 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1507 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 | ENSCJAG00000010938 | 1 retrocopy |
retro_cjac_1507 ,
|
| Callithrix jacchus | ENSCJAG00000020681 | 1 retrocopy |