RetrogeneDB ID: | retro_mmul_2279 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 8:6802355..6804104(+) | ||
| Located in intron of: | ENSMMUG00000018668 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTPN4 | ||
| Ensembl ID: | ENSMMUG00000005610 | ||
| Aliases: | None | ||
| Description: | tyrosine-protein phosphatase non-receptor type 4 [Source:RefSeq peptide;Acc:NP_001253553] |
Retrocopy-Parental alignment summary:
>retro_mmul_2279
CGCTACTAGTATTTTTTACAAATTTAACAAGACATTCTTACTGGAAGATTGCCCTGTTCTTACGATACTACTGCCCTTTT
TCCTTTATTTGCTGTTCAGACTAAACTTGGAGACTACAGTCAGTCAGAGAACTTGCTAGGCCACCTCTCAGGTTATTCTT
TCATTCCTGATCATCCTCAAAAATTTGAAAAATAAATTGTAAAAATGACATCAGCAACATATAGGCTTATGTCCTTGAGA
AGCAGAAGTTAATTACCTAAACACAGCAAGTACCTTAGAACTCGGTGGAGTTGAATTCCACTATGCAAGGAATCGAAGTT
ACAATGAAATTATGATTGGAATGACGTCAAGAGAAATTCTGATTTATAAGAGACTACGAATGAGTACCTTTCCGTGGTTG
AAGATTGTAAAAATTTGTTTTAAGTGCAAACAGTTTTTTATTCAGCTTTGAAAATGGCTTGCATAAATCTGGAGAAAGAT
TATCAGGATTTAATATGATAAATTGTGGAGCATGTAAACGTTTGTGGAAAGCAAGTTTAGAACATCACATATTCTTCTGT
TTGGACAGACCACTTCCAACTAGAAATAATTCTTTTGCACATTATTTTACATTAGGTTCAAAATTCCTAATGCACCGTGG
GAGAACTGAAGTTCAGTTAATTCAGTATGGCAAATAAAAGGCAAATAAAGACAATTTGCAGGATCCTCAAGTAAGCCATT
GACGTGGAAATTAATGAATTGGGAAGTAGTAAGCAGGAATTCAATATCTGATGAAAGGATTGGAAACGTAAAGCCTTCCA
TCACAGCTGCCACCTGGAACAGGAATTTCTACTCATCAAAATTTTGCATTCATACAAGAGGGAACCTGATTATGACCGTC
TTCAGTTGGTCATTTGGTAGATTATGTGGTTCACACTTCTTCCAAAGTATTTGCGAATCAGAGATCACCATTATCAGCAC
AAGCTGATAGCATCACTCTGGAATCATCCACCATTACAGGACACCCCTGAGATAGGTAGTCTCCGGCTTTACCACCCAAA
CAATCTAAGAAAAACAGTTGGAACCAAATTCATTATTTACATTTCCAACAAGATCTGGAAGATCATATTAATGAAACATT
GATATTACATCTTCTCTTAAAAAATCTACTCCTAATGGTGGTGTTCTACATGATCATCTTGTTCTAATCAGAGTGAACCT
GATGAAAATGGAAGGTATGGAGTCAATGTAAAGGGGAATATGGTCAGAAGATGTCTGTGATCGTGTCCTGAGAAGCACCA
GGAACACCTTTGAACTCGGTGACCCTCGATTGAAGAGAAGACCTAGTTGTATTGATCAGTGGTTGGGACTTTACAGACTC
ATCCATGATTGGTTTGTCCTGCTTATTAAAGCTAACTGTGAGAGACATTCTGGGGAACTCATGCTTCTAGTTCTACCTGT
GCTGCATATGATGTAGTGGAAGAAGTGCTAGAAAACGGGACAGACTTCCAGTACATTCTGGAGAAAGACCCACTAGATAG
TGTCCACCAGGATGACCGTTTCCTGTGGGAGTCAGTGATCCAGCTAGCCAAGGGCTTACCGCTGGAACATTCTGGACACA
ATTTGATCAGCTTATCAAAAAGAAAACTTGGAATGACAATGTCTGGTGCCAGATTACCTTAGAACCTTTCCAAAAATAGA
TACAGAGATAGTTTGCCTTATGATACTACATGGATTATTTTAAAAGGTAATGAGGACTACATCAGTGCA
ORF - retro_mmul_2279 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.39 % |
| Parental protein coverage: | 63.17 % |
| Number of stop codons detected: | 15 |
| Number of frameshifts detected: | 11 |
Retrocopy - Parental Gene Alignment:
| Parental | RYQYFLQIKQDILTGRLPCPSNTAALLASFAVQSELGDYDQSENLSGYLSDYSFIPNQPQDFEKEIAKL- |
| RY.YFLQI.QDILTGRLPC...T.AL...FAVQ..LGDY.QSENL.G.LS.YSFIP..PQ.FEK.I.K.. | |
| Retrocopy | RY*YFLQI*QDILTGRLPCSYDTTALFPLFAVQTKLGDYSQSENLLGHLSGYSFIPDHPQKFEK*IVKM> |
| Parental | HQQHIGLSPAEAEFNYLNTARTLELYGVEFHYARDQSNNEIMIGVMSGGILIYKNRVRMNTFPWLKIVKI |
| HQQHIGL.P.EAE.NYLNTA.TLEL.GVEFHYAR..S.NEIMIG..S..ILIYK.R.RM.TFPWLKIVKI | |
| Retrocopy | HQQHIGLCP*EAEVNYLNTASTLELGGVEFHYARNRSYNEIMIGMTSREILIYK-RLRMSTFPWLKIVKI |
| Parental | SFKCKQFFIQLRK-ELHESRETLLGFNMVNYRACKNLWKACVEHHTFFRLDRPLPPQKN-FFAHYFTLGS |
| .FKCKQFFIQL.K..LH.S.E.L.GFNM.N..ACK.LWKA..EHH.FF.LDRPLP...N.FF...F.... | |
| Retrocopy | CFKCKQFFIQL*K>GLHKSGERLSGFNMINCGACKRLWKASLEHHIFFCLDRPLPTRNN<FFCTLFYIRF |
| Parental | KFRYCGRTEVQSVQYGKEKANKDRVFARSPSKPLARKLMDWEVVSRNSISDDR-LETQSLPSRSPPGT-- |
| K..........SV........K.R.FA.S.SKPL..KLM.WEVVSRNSISD.R.LET.SLPS..PPGT.. | |
| Retrocopy | KIPNAPWEN*SSVNSVWQIKGK*RQFAGSSSKPLTWKLMNWEVVSRNSISDER>LET*SLPSQLPPGTGI |
| Parental | PNHRNSAFTQEGTRLRPSSVGHLVDHMVHTSPSEVFVNQRSPSSTQANSIVLESSPSQETPGDGKPPALP |
| ..H.N.AF.QEGT.L.PSSVGHLVD..VHTS.S.VF.NQRSP.S.QA.SI.LESS.....P.D...PALP | |
| Retrocopy | STHQNFAFIQEGT*L*PSSVGHLVDYVVHTS-SKVFANQRSPLSAQADSITLESSTITGHP*DR*SPALP |
| Parental | PKQSKKNSWNQIHYSHSQQDLESHINETF-DIPSSPEKPTPNGGIPHDNLVLIRM-KPDENGRFGFNVKG |
| PKQSKKNSWNQIHY.H.QQDLE.HINET..DI.SS..K.TPNGG..HD.LVLIR...PDENGR.G.NVKG | |
| Retrocopy | PKQSKKNSWNQIHYLHFQQDLEDHINETL<DITSSLKKSTPNGGVLHDHLVLIRV<EPDENGRYGVNVKG |
| Parental | G-YDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHT-HDQVVLFIKASCERHSGELMLLVR |
| ..Y.QKM.VIVS..APGTP.........E.D.VVLI.G.D......HD..VL.IKA.CERHSGELMLLV. | |
| Retrocopy | N<YGQKMSVIVS*EAPGTPLNSVTLD*RE-DLVVLISGWDFTDSS<HDWFVLLIKANCERHSGELMLLVL |
| Parental | PN-AVYDVVEEKLENEPDFQYIPEKASLDSVHQDDHSLRESMIQLA-EGLITGTVLTQFDQLYRKKP-GM |
| P..A.YDVVEE.LEN..DFQYI.EK..LDSVHQDD..L.ES.IQLA..GL..GT..TQFDQL..KK..GM | |
| Retrocopy | PV<AAYDVVEEVLENGTDFQYILEKDPLDSVHQDDRFLWESVIQLA<QGLTAGTFWTQFDQLIKKKT>GM |
| Parental | TMSCAKLPQNISKNRYRDISPYDATRVILKGNEDYINA |
| TMS.A.LP.N.SKNRYRD..PYD.T..ILKGNEDYI.A | |
| Retrocopy | TMSGARLP*NLSKNRYRDSLPYDTTWIILKGNEDYISA |
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 | 32 .16 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .48 RPM | 26 .58 RPM |
| SRP007412_cerebellum | 0 .32 RPM | 36 .94 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .00 RPM |
| SRP007412_kidney | 0 .12 RPM | 5 .52 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .64 RPM |
| SRP007412_testis | 1 .24 RPM | 17 .75 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2279 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2279 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_2279 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001015 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000005610 | 1 retrocopy |
retro_mmul_2279 ,
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