RetrogeneDB ID: | retro_mmul_2013 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 6:72085095..72086121(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMU.18525 | ||
| Ensembl ID: | ENSMMUG00000023163 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mmul_2013
ATGAGCAAGCTGAACCACAATCTCTAGGAGGTGATGAGCAAACTGGAGAAGCAACATTCCAATAAAGTGTTTGTGGTAAA
GGGACTATCAAGCAGCAGCAGGCGCTCTTTAGTCATTTCTCCCCCGGTTCAAACATCTGTGGTCTCCAGTCCTCTTGCCT
CACCTACTAGTCCCTCTACACTTTCCTTGAAGAGTGAGAGTGAATCTGTCTCAACAACTGAAGATCTGGCACCTGATGCA
GCCCAGGGGGAAGATAATTGTGAGATCAAGGAGCCCTTAGAAGATGAAGAAATAGAAAAGGAAGAATCTGAAGCAAGCTT
CTCTGAGGAAGAAGAGCCTCTACCAGCCTGCAATAGCCCCACCCAGGCCCAGCCCTCGCCTACCATTGAGAGTGGCAAGT
CCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCTCCATCACCAGGCAGAGCCCTGCGTCCTTCAAGGCAGCCTGCATTATCT
GCCACAGAAGTAGTCCTCCGAACTCGCACCACAAGTGAAGGATTTGAACAACCAAAGAAGAGAGCCTCTCTCCAGAGGAC
CTCAGCACCCCCTAGTAGGCCTCCTCCACCCAGAGACACTCCAAGCCCCAGGCCCTCCTCAGGGAACATACCCTCCAGCC
CTCCAGCCTCTTGAGGGGATTCACCCACCAGCCCTAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGGACCTCCCTA
GAGGTCTCTCCTAATCCAGAACCACCAGAGAAACCAGTAAGAACTCCTGAGGCCAAAGAAAATGAAAACATCCACGATCA
GAACCCCGAAGAACTTTGCACTTTTCCCACCTTAATGACATCTCAGATTGCTTCAGAACCTGGAGAGGCAAAGAAGATGG
AAGATAAGGAAGAGGATAATAAGCTTGTCTTAGCTGACTCCTCAGAGGGCCAAGACCAGTTTAAAGTCTCCATGGTACCA
GACCAGAGCAACTTCGCAGCACCTGAACCTCAAGAAGAGGTACCTACCAGTGAAAATGCACAACTC
ORF - retro_mmul_2013 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.38 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSS-RRSLVISPPVQTTMVSSPLTSPTSPSTLSLKSESESV |
| MSKLNHNL.EVMSKLEKQHSNKVFVVKGLSSS.RRSLVISPPVQT..VSSPL.SPTSPSTLSLKSESESV | |
| Retrocopy | MSKLNHNL*EVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPVQTSVVSSPLASPTSPSTLSLKSESESV |
| Parental | SATEDLAPDAAQGDDNSEIKELLEDEEIEKEGSEASSSEEEEPLPACNGPAQAQPSLTIESVKSQEEVLP |
| S.TEDLAPDAAQG.DN.EIKE.LEDEEIEKE.SEAS.SEEEEPLPACN.P.QAQPS.TIES.KSQEEVLP | |
| Retrocopy | STTEDLAPDAAQGEDNCEIKEPLEDEEIEKEESEASFSEEEEPLPACNSPTQAQPSPTIESGKSQEEVLP |
| Parental | SSPAPSPGEAPSPSGQPSSSAAEVVLRTRTASEGSEQPKKTASLQRTSAPPSRPPPPRATASPRPSSGNI |
| SSPAPSPG.A..PS.QP..SA.EVVLRTRT.SEG.EQPKK.ASLQRTSAPPSRPPPPR.T.SPRPSSGNI | |
| Retrocopy | SSPAPSPGRALRPSRQPALSATEVVLRTRTTSEGFEQPKKRASLQRTSAPPSRPPPPRDTPSPRPSSGNI |
| Parental | PSSPPASGGGSPTSPRASLGTGTPSPRTSLEVSPNPETPEKPVRTPEAKENENMNNQNPEELCTSPTLMT |
| PSSPPAS.G.SPTSPR.SLGT.TPSPRTSLEVSPNPE.PEKPVRTPEAKENEN...QNPEELCT.PTLMT | |
| Retrocopy | PSSPPAS*GDSPTSPRVSLGTETPSPRTSLEVSPNPEPPEKPVRTPEAKENENIHDQNPEELCTFPTLMT |
| Parental | SQIASEPGEAKKMEDKEEDDKLISVDSSEGQDQLQVSAVPENNNLTAPEPQEEVSTSENPQL |
| SQIASEPGEAKKMEDKEED.KL...DSSEGQDQ..VS.VP...N..APEPQEEV.TSEN.QL | |
| Retrocopy | SQIASEPGEAKKMEDKEEDNKLVLADSSEGQDQFKVSMVPDQSNFAAPEPQEEVPTSENAQL |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 3 .36 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 2 .30 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .58 RPM |
| SRP007412_heart | 0 .00 RPM | 3 .06 RPM |
| SRP007412_kidney | 0 .00 RPM | 15 .14 RPM |
| SRP007412_liver | 0 .00 RPM | 8 .23 RPM |
| SRP007412_testis | 0 .00 RPM | 63 .48 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2013 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2013 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2013 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3192 |
| Pan troglodytes | retro_ptro_2251 |
| Gorilla gorilla | retro_ggor_1336 |
| Pongo abelii | retro_pabe_2648 |
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000023163 | 1 retrocopy |
retro_mmul_2013 ,
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