RetrogeneDB ID: | retro_mmul_2050 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 6:151755681..151756541(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OBFC1 | ||
| Ensembl ID: | ENSMMUG00000015323 | ||
| Aliases: | None | ||
| Description: | CST complex subunit STN1 [Source:RefSeq peptide;Acc:NP_001253519] |
Retrocopy-Parental alignment summary:
>retro_mmul_2050
ACTGGAGTTATAAACTGCATCTGCTAGAAAATACTGAGCAATGTCAAGTTTTTATCCATTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGATACCATTGAGCAGAGAATAAAAATTGAAATTGGGGACATGTTCT
GAATCAGAGGCTATGTCCGCACATGCAGAGAAGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGCATTTGAGCTGCCCGTTAATCTACAGGAAAGTTTAGACCAAGTCTTTCCATAGCCCAG
ACTTAGAGAAAGAAGCACTAAGCAAACCAGGTGCCCTGGCCCTCACTAGTCTCATGCATTTGCTGAGCGAAAAAGCCAAA
GAATTCCCCATGGAGAACAGAGTGCAGACCTTTGACCAACAGGAGTTGGAAATGGTGGAGGCTTTGCTGTCCCTTGCTAA
CCAGCCTCTTACTGACAGCACCTGCTCTGACCTAGGGAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCATAT
TTTAAAATGTTATGCAACAGCTGCAGGAAAAAGGACTTGTTTTCCAGAAAGATGGTGGTTTTCATAACCTATGCTGTGTA
ACCAGAACAGACAAAGACCTGCATAGGAAAATCCACTGGATAATTCAGGAAGACTGCCAGAAACCAAATCACCCGAAGAA
GGGCTGCCACTTCCTGCACATCTTGGCCTGCACTCACCCTGATCATCTGCCCAGTCCTAGGTAGGGCTATGCTGCAGCAA
GTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAACACAATGGAGCACCACTATTCC
ORF - retro_mmul_2050 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.28 % |
| Parental protein coverage: | 77.72 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIERRTKIEIGDTIRVRGSIRTYREEREIHA |
| TGVINCIC.K.L.N....S.AP.AARELS.TS.LKKLQ.TIE.R.KIEIGD....RG..RT.REE.EI.A | |
| Retrocopy | TGVINCIC*KILSNVKFLSIAPNAARELSFTSILKKLQDTIEQRIKIEIGDMF*IRGYVRTCREE*EIYA |
| Parental | TAYYKVDDPVWNIQIARMLELPT-IYRKIYDQPFRSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME |
| TAYYKVDDPVWNIQIAR..ELP..IYRK.....F.S..LEKE.ALS.PGAL.L.SL..LLSEKAKEF.ME | |
| Retrocopy | TAYYKVDDPVWNIQIARAFELPV>IYRKV*TKSFHSPDLEKE-ALSKPGALALTSLMHLLSEKAKEFPME |
| Parental | NRVQSFYQQELEMVESLLCLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLREKGLVFQKDDGFD |
| NRVQ.F.QQELEMVE.LL.LANQP...S.CSD..NFKKD.T.KAI.SIF.N..Q.L.EKGLVFQKD.GF. | |
| Retrocopy | NRVQTFDQQELEMVEALLSLANQPLTDSTCSDLGNFKKDITFKAIYSIF*NVMQQLQEKGLVFQKDGGFH |
| Parental | NLYYVTREDKDLHRKIHQIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI |
| NL..VTR.DKDLHRKIH.IIQ.DCQKPNH..KGCHFLHILAC...L.I.P.L..A.LQQVLELLEDQSD. | |
| Retrocopy | NLCCVTRTDKDLHRKIHWIIQEDCQKPNHPKKGCHFLHILACTH>LIICPVLGRAMLQQVLELLEDQSDL |
| Parental | VSTMEHYYT |
| ..TMEH.Y. | |
| Retrocopy | INTMEHHYS |
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 .11 RPM | 6 .84 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .08 RPM | 4 .68 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .46 RPM |
| SRP007412_heart | 0 .06 RPM | 19 .73 RPM |
| SRP007412_kidney | 0 .00 RPM | 14 .55 RPM |
| SRP007412_liver | 0 .04 RPM | 9 .26 RPM |
| SRP007412_testis | 0 .04 RPM | 29 .93 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2050 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2050 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2050 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3257 |
| Pan troglodytes | retro_ptro_2203 |
| Gorilla gorilla | retro_ggor_2219 |
| Pongo abelii | retro_pabe_2701 |
| Callithrix jacchus | retro_cjac_1791 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018342 | 1 retrocopy | |
| Homo sapiens | ENSG00000107960 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000008979 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000015323 | 1 retrocopy |
retro_mmul_2050 ,
|
| Nomascus leucogenys | ENSNLEG00000015282 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000002628 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000002919 | 1 retrocopy |