RetrogeneDB ID: | retro_mmul_1853 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 4:124136470..124137766(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIP4 | ||
| Ensembl ID: | ENSMMUG00000009882 | ||
| Aliases: | None | ||
| Description: | activating signal cointegrator 1 [Source:RefSeq peptide;Acc:NP_001253149] |
Retrocopy-Parental alignment summary:
>retro_mmul_1853
CAGTGCTTCCAAAAAGATGAAACTTTAGATGGGCAGAAATCAAGGGACCAGCTAAAGCTGGGTAGGAGGAAAGGGAGAGA
CAGACAGGAAGTTCCTGTATTTGCTGAACCTGACACAACTGCAGAGGTAAAACACCTTTTAATTTGCCCAAGGCATGAGA
GAACAGCAACTCCTTTAAGAGTAAGACAAAGTTTGTCAATTTACACACAAGAGAGGGACCCACAGGCTTGCAGTCTGCTC
CCGGGTTGCCATCCTTGTGATTGCCTGGGCCAGAAGTACAAGCTCATCAGTAGCTGTCTGATCTGTGGGCCTGTTGTTTG
TGAAAAAGAGGGTGCCAGCCCTTGCTTATTCTGTGTCACAACAGTATGTACTCATGAAGAACAGGATATTTTGCAGCATG
AGTCAAATGAGAGCCAGAAACTGCTAAAGAAGCTTATGCCATTGATGGAGAATTCTGGAAAGGTGGACAACTCTGCCAAG
GACTTTCTATGTCATTGAGAATTTCAAATTATGTCTGGTCTGGAGAAGGATATCAAGCACAAAGACAGGCTGTTAGAGTT
GCACAGAGCTAGTTTTCAAAGGACCCAAGTCATTGATGCTGATCAGATTTTTTTGCCAGTGACTCTAACCAGTGGTTTTC
CAAACTTGAGTGGGAAACCAAATGAGAAGCAAGAAGAGGAGCTGAGAGAACTTCGACATGCCTCTTGACTCTCTAAGAAG
GTCACCATTGAGTTTACAGCAGGAAGATCCTGGAAGAAGAAAATCCATTAGCAGAATATCACAGCAGACTAGACGAGACA
ATACAGGCCATTGCTAAGGAAACCTTGAATGAGACACTGACCCCATTTTATATATCTCCTGAAGAGCCTTTGGGAGTTCT
GGTAAATCTCAGCACATACCAGTCCCCTCCCCAGTGGGTTGACCATGCAGGTGCAGCCTCACAGAATAAGGCTTTCCATT
CAGCAGGATTGGGACTGGAATTCAACTCATTTCAGTACTTCTTGTGAATCCAGGACCAAGACTTTCAGGGAGGTTTGACA
GTGGCTCATGTCTCTCTATACATCAGGCCTGGGTTTCTCAGCTTGTTAGAGGGATTAGAAAATGATGGAGTGCAGATCCT
GGTATATCTCCCACAGAGGACAACTTTGGATAGCAGTCGTAGCCAAAACCTCCCTCTGCCTTCAAGAAGTCTCAGAACTC
CAGGTTACGTATCATCTTCTTCATGGGAAAGATGTGGAATTCCCCAGTGACTATCCATCAGGTTGTCTTTTGGGCTGTCT
GGACCTAATTGCTTGT
ORF - retro_mmul_1853 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.62 % |
| Parental protein coverage: | 74.35 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 9 |
Retrocopy - Parental Gene Alignment:
| Parental | QCFKKDEILDGQKSGDHLKRGRKKGRNRQEVPAFTEPDTTAEVK-TPFDLAKAQENSNSVKKKTKFVNLY |
| QCF.KDE.LDGQKS.D.LK.GR.KGR.RQEVP.F.EPDTTAEVK.TPF.L.KA.ENSNS.K.KTKFVNL. | |
| Retrocopy | QCFQKDETLDGQKSRDQLKLGRRKGRDRQEVPVFAEPDTTAEVK<TPFNLPKA*ENSNSFKSKTKFVNLH |
| Parental | TREGQD-RLAV-LLPGRHPCDCLGQKHKLINNCLICGRIVCEQEGSGPCLFCGTLVCTHEEQDILQRDSN |
| TREG...RLAV.LLPG.HPCDCLGQK.KLI..CLICG..VCE.EG..PCLFC.T.VCTHEEQDILQ..SN | |
| Retrocopy | TREGPT<RLAV<LLPGCHPCDCLGQKYKLISSCLICGPVVCEKEGASPCLFCVTTVCTHEEQDILQHESN |
| Parental | KSQKLLKKLMSGVENSGKVDISTKDLLPHQELRIKSGLEKAIKHKDKLLEFDRTSIRRTQVIDDE-SDYF |
| .SQKLLKKLM...ENSGKVD.S.KD.L.H.E..I.SGLEK.IKHKD.LLE..R.S..RTQVID...SD.F | |
| Retrocopy | ESQKLLKKLMPLMENSGKVDNSAKDFLCH*EFQIMSGLEKDIKHKDRLLELHRASFQRTQVIDAD<SDFF |
| Parental | ASDSNQWLSKLERETL-QKREEELRELRHASRLSKKVTIDFAG-RKILEEENSLAEYHSRLDETIQAIAN |
| ASDSNQW.SKLE.ET...K.EEELRELRHAS.LSKKVTI.F...RKILEEEN.LAEYHSRLDETIQAIA. | |
| Retrocopy | ASDSNQWFSKLEWETK>EKQEEELRELRHAS*LSKKVTIEFTA<RKILEEENPLAEYHSRLDETIQAIAK |
| Parental | GTLNQPLTKLDRSSEEPLGVLVNPNMYQSPPQWVDHTGAASQKKAFRSSGLGLEFNSLQHQLRIQDQEFQ |
| .TLN..LT....S.EEPLGVLVN...YQSPPQWVDH.GAASQ.KAF.S.GLGLEFNS.Q..L.IQDQ.FQ | |
| Retrocopy | ETLNETLTPFYISPEEPLGVLVNLSTYQSPPQWVDHAGAASQNKAFHSAGLGLEFNSFQYFL*IQDQDFQ |
| Parental | EG-FDGGWCLSIHQPWASL-LVRGI-KRVEGRSWYTPHRGRLWIAATAKKP-SPQEVSELQATYRLLRGK |
| .G.FD.G.CLSIHQ.W.S..L..G..K..E.RSWY..HRG.LWIA..AK.....QEVSELQ.TY.LL.GK | |
| Retrocopy | GG<FDSGSCLSIHQAWVSQ>LLEGL>KMMECRSWYISHRGQLWIAVVAKTSLCLQEVSELQVTYHLLHGK |
| Parental | DVEFPNDYPSGCLLGCVDLTDC |
| DVEFP.DYPSGCLLGC.DL..C | |
| Retrocopy | DVEFPSDYPSGCLLGCLDLIAC |
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 | 6 .84 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 3 .65 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 7 .04 RPM |
| SRP007412_heart | 0 .00 RPM | 7 .13 RPM |
| SRP007412_kidney | 0 .12 RPM | 12 .79 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .12 RPM |
| SRP007412_testis | 0 .00 RPM | 26 .42 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1853 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1853 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_1853 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000032766 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000009882 | 1 retrocopy |
retro_mmul_1853 ,
|
| Oryctolagus cuniculus | ENSOCUG00000002322 | 1 retrocopy |