RetrogeneDB ID: | retro_cjac_3040 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:155327135..155328075(-) | ||
| Located in intron of: | ENSCJAG00000005653 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RBMX2 | ||
| Ensembl ID: | ENSCJAG00000002436 | ||
| Aliases: | None | ||
| Description: | RNA binding motif protein, X-linked 2 [Source:HGNC Symbol;Acc:24282] |
Retrocopy-Parental alignment summary:
>retro_cjac_3040
AAGGCGAAGCCGATCAACCAACTGAATGAGTGACAGGTCCAGCCTGGGGTGGTCGATAAGGTGTCCTGTGACTCCAAGTG
CAAGGACGGCGCCTGGATCTTCCTGGGAGGGCTTCCTTATGAACTGAATGAAGGGGACATCATCTGTGTGTTCTCACAAC
ATGGCGAGATTGTTAACATTCATCTTGTGCCGGACAAAAGAATGGGAAATCCAAAGGATTCCATTTCCTCTCCTAGGGAG
ACCAGAGGAGCACAATTCTGGCTGTTGACAATTTAAATGGGATTAAGATCAAAGGAAGAACTATCTGAGTGGATCAAGTG
TCTAACCACCGAGTACCTAAGGAGTCAGGAGAAATAGAGGATGTCACCCGAGAGCTCCAGAGAAGGGCTGTGGGGCTCGT
ACTTCCTCACCAAGTTTGTCTCAGAGCTCCGAAAATGACAAACCAACACAAAAGCACAAAAAAGACAAACAGGAAAAAAA
GGAAAGAAAGAAAGAGAGAAAACTGACTGGGAGGTACAGGCAGTGCAACCATCCTCTTCATCATTCGGAAACGAGACAGC
AAAGGAAAAGGATGACCTGGCCCTAAGAAACACAGCAACAAGAACTCAGAGATAGCTCAGAAGCCAGAGCCCAGGGAGGG
GCGGAAGCTCCCCGGGGCCAGGACTGCCTACTCTGGTGGAGCAGAGGACCTAGAGCCGGAGCTGAAGGAGGAGAAATCGA
ACCACAAGCCTAAGTCCTCAAGCAGGAGAGAGGCAAAAGAAAAGACCAGGGATAGGGACAGAGGGCGGAGTCAGACACAC
ATTGTAGCCTGTACAACGGGCGTTCTGAAGGGTGTAGTCATGGGGTTGAAGTAGGAGCTGAGATAAATCTCAGAGGCATA
AAAGGGCCTGGCGCTCCCGGGAGCCTTCGAATCCCAGTGACCATAGGCTTCAGTGAAGAT
ORF - retro_cjac_3040 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.22 % |
| Parental protein coverage: | 91.14 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | KVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGEIVNINLVRDK-KTG |
| K.K.IN.LNE..VQ.GV.DKVS..S..KD.AWIFLGGLPYEL.EGDIICVFSQ.GEIVNI.LV.DK.K.G | |
| Retrocopy | KAKPINQLNE*QVQPGVVDKVSCDSKCKDGAWIFLGGLPYELNEGDIICVFSQHGEIVNIHLVPDK<KNG |
| Parental | KSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKDSEEMDDVTRELQ-EKGCGARTPSP |
| KSKGF.FL...DQRSTILAVDN.NGIKIKGRTI.VD.VSN.R.PK.S.E..DVTRELQ.EKGCGART.SP | |
| Retrocopy | KSKGFHFLS*GDQRSTILAVDNLNGIKIKGRTI*VDQVSNHRVPKESGEIEDVTRELQ<EKGCGARTSSP |
| Parental | SLSKSSEDEKPTKKHKKDKKEKKKRKKEKEKTDREIQAEQP-SSSSPRSKTVKKKDD-PGPKRHSSKNSE |
| SLS.SSE..KPT.KHKKDK.EKK.RKKE...T.R..Q...P.SSS.....T.K.KDD.PGPK.HS.KNSE | |
| Retrocopy | SLSQSSENDKPTQKHKKDKQEKKERKKERKLTGRYRQCNHP<SSSF-GNETAKEKDD<PGPKKHSNKNSE |
| Parental | RAQKSEPREGQKLPKARTAYSGGAEELERELKKEKPKHEHKSSSKREAREEKTRDRDRRRAQTHILASTT |
| .AQK.EPREG.KLP.ARTAYSGGAE.LE.ELK.EK..H..KSSS.REA..EKTRDRDR.R.QTHI.A.TT | |
| Retrocopy | IAQKPEPREGRKLPGARTAYSGGAEDLEPELKEEKSNHKPKSSSRREAK-EKTRDRDRGRSQTHIVACTT |
| Parental | GVPKGIVI-EVEVGAEINPIGIKGPGAPGSGSLPIPVTVGVTED |
| GV.KG.V...VEVGAEIN..GIKGPGAP..GSL.IPVT.G..ED | |
| Retrocopy | GVLKGVVM<GVEVGAEINLRGIKGPGAP--GSLRIPVTIGFSED |
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 .60 RPM | 2 .31 RPM |
| SRP051959_heart | 0 .30 RPM | 3 .56 RPM |
| SRP051959_kidney | 0 .27 RPM | 3 .95 RPM |
| SRP051959_liver | 0 .22 RPM | 2 .75 RPM |
| SRP051959_lung | 0 .59 RPM | 4 .98 RPM |
| SRP051959_lymph_node | 0 .34 RPM | 4 .09 RPM |
| SRP051959_skeletal_muscle | 0 .35 RPM | 4 .98 RPM |
| SRP051959_spleen | 0 .21 RPM | 4 .08 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3040 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3040 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3040 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002436 | 2 retrocopies |
retro_cjac_3040 , retro_cjac_4128,
|
| Equus caballus | ENSECAG00000008257 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000001763 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000017095 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000016412 | 1 retrocopy |