RetrogeneDB ID: | retro_mmul_2139 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 7:28113718..28114838(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RLIM | ||
| Ensembl ID: | ENSMMUG00000009249 | ||
| Aliases: | None | ||
| Description: | E3 ubiquitin-protein ligase RLIM [Source:RefSeq peptide;Acc:NP_001253768] |
Retrocopy-Parental alignment summary:
>retro_mmul_2139
ATGGAAAACTCAGATTCTAACGACAAAGGAAGTGGTGATCAGTCTGCAGCACAGCGCAGAATTCAGATGGACCGATTGGA
TCGGGAAGAAGCTTTCTACCAATTTGTAAATAACCTGAGTGAAGAAGATTATAGGCTTAGGAGAGAGAACAGTTTGCTAG
GCACCCCAGGTGAAAGTACTGAGGAACAGTTGCTGAGAAGACTACAGCAAATTAAAGAAAGCCCGCCACCGCAAAACTCA
GGTGAAAATAGAGGAGGAGACTCTTCAGATGATGTGTCTAATGGTGACTCTACAACAGACTGGCTTAACTCTGTCAGACA
AACGGAAAATATAACAAGAAGTGGAAAAAGAGGAAACCAATCTTGGAGAGCAGTGAGCCGGACTAATCCAAACAGTGGTG
ACTGCAGATTCAGTTTAGAGATAAATGTTAACAGTAATAATGGGGGCCAAATTTCAGAGAATGAAAATGAGCCATCTGCA
AGACGTTCTAGTGGAGAAAATGTGGAAAACAACAGCCAAAGGCAAGTGGAAAACCCACGACCTGAATAGTATCTGCAAGG
CCATCTAGATCAGAACGAAATTCAGCTGAAGCATTAACAGAAGTTCCACTTACCAGAGGTCAGAGGAGGGCAGGAAGCAG
GAGGCTAGACTATCGGAGAACCAGAGCAAGAGCTGAGAGAAGGAGGTCACCTCTGCATCCAATGAGTGAAATTCCACGAA
GATCTCATCATCATATCTCATCTCAGATTTTTGAACATCTTTGGTAAATGAGACGGAGGGAAGTTCTAGAACCCGGCCCC
GTGTGACATTGAGAGAGCAAATATCTGGGCCTGAGTTGCTAAGTAGAGGTATTTTTGCAGCTTCTGGAACAAGAAATGCC
TCTCAAGGAGCAGGTTCTTCAGACACAGCTGCCAATGGTGAATCTACAGGATCAGGATAGAGACCAACCGTAGTCCTTGA
TCTTCAAGTAAGAAGAGTTCGTCCTGGAGAATATCAGCAGAGAGAGAGAATAGTCAGCGAAACGTGGTCTAGGTCTCAGA
CGCCAAACAATACTGTCACCTACGAAAGTGAACGAGGAGGTTTTAGGTGTACATTTTCACGTTCTGAGCAGGGAGGTGTG
ORF - retro_mmul_2139 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.53 % |
| Parental protein coverage: | 60.1 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTEEELLRRLQQ |
| MENSDSNDKGSGDQSAAQRR.QMDRLDREEAFYQFVNNLSEEDYRL.R.N.LLGTPGESTEE.LLRRLQQ | |
| Retrocopy | MENSDSNDKGSGDQSAAQRRIQMDRLDREEAFYQFVNNLSEEDYRLRRENSLLGTPGESTEEQLLRRLQQ |
| Parental | IKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQSWRAVSRTNPNSGDFRFSLE |
| IKE.PPPQNS.ENRGGDSSDDVSNGDS..DWLNSVRQT.N.TRSG.RGNQSWRAVSRTNPNSGD.RFSLE | |
| Retrocopy | IKESPPPQNSGENRGGDSSDDVSNGDSTTDWLNSVRQTENITRSGKRGNQSWRAVSRTNPNSGDCRFSLE |
| Parental | INVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPRSE-STSARPSRSERNSTEALTEVPPTRGQR |
| INVN.NNG.Q.SENENEPSARRSSGENVENNSQRQVENPR.E...SARPSRSERNS.EALTEVP.TRGQR | |
| Retrocopy | INVNSNNGGQISENENEPSARRSSGENVENNSQRQVENPRPE<IVSARPSRSERNSAEALTEVPLTRGQR |
| Parental | RARSRSPDHRRTRARAERSRSPLHPMSEIPRRSHHSISSQTFEH-PLVNETEGSSRTRHHVTLRQQISGP |
| RA.SR..D.RRTRARAER.RSPLHPMSEIPRRSHH.ISSQ.FEH..LVNETEGSSRTR..VTLR.QISGP | |
| Retrocopy | RAGSRRLDYRRTRARAERRRSPLHPMSEIPRRSHHHISSQIFEH<SLVNETEGSSRTRPRVTLREQISGP |
| Parental | ELLSRGLFAASGTRNASQGAGSSDTAANGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQ |
| ELLSRG.FAASGTRNASQGAGSSDTAANGESTGSG.R.PT.VLDLQVRRVRPGEY.QR..I.S.T.SRSQ | |
| Retrocopy | ELLSRGIFAASGTRNASQGAGSSDTAANGESTGSG*R-PTVVLDLQVRRVRPGEYQQRERIVSETWSRSQ |
| Parental | TPNNTVTYESERGGFRRTFSRSERAGV |
| TPNNTVTYESERGGFR.TFSRSE..GV | |
| Retrocopy | TPNNTVTYESERGGFRCTFSRSEQGGV |
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 .78 RPM | 31 .60 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .24 RPM | 23 .32 RPM |
| SRP007412_cerebellum | 0 .39 RPM | 20 .79 RPM |
| SRP007412_heart | 0 .06 RPM | 6 .30 RPM |
| SRP007412_kidney | 0 .23 RPM | 7 .04 RPM |
| SRP007412_liver | 0 .04 RPM | 2 .65 RPM |
| SRP007412_testis | 3 .54 RPM | 10 .03 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2139 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2139 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2139 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1495 |
| Pan troglodytes | retro_ptro_1014 |
| Pongo abelii | retro_pabe_1245 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000131263 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000009249 | 1 retrocopy |
retro_mmul_2139 ,
|
| Pongo abelii | ENSPPYG00000020481 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000022037 | 1 retrocopy |