RetrogeneDB ID: | retro_btau_447 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 11:60336077..60337597(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | POMGNT1 | ||
| Ensembl ID: | ENSBTAG00000013322 | ||
| Aliases: | None | ||
| Description: | protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 [Source:RefSeq peptide;Acc:NP_001019656] |
Retrocopy-Parental alignment summary:
>retro_btau_447
CCTCATATAGATGAGACCATGGTGCTGTTCCTCAACATGATGGCACCTGGCCAAGGGTTCACCTGCATTATTAAGGACAC
AGGCTCCTTCCATCTCAAGGACACAGCCAAGGCTCTGCTGAGGAGGCGCGACAGCCAGGCTGGCCCTGCCCTGGGCTGGA
AAGAGACCTGGGCCTTCGTGGGATGAAAAGGAGATCCTATCCTTGGGGAGAAACATTCTGACTCACCTGCCCTCTCCTCC
TGCGGGGGTTCAGTTCTGCTGAAGACAGATGTGCCACTAAGCTCAGCTGAAGAGGCAGAGATGAAGATGTGCCACTGGGC
AGACATGGAGCTGAACCATCACAGCTGCTGCTTCTGCAGCAAAATCAAGGGCGACGGGAACATGTACAGCTGCAAGGACC
CCACACCTTCCCAGTTCAGCCCTGACCCACCCCAGACAACAAGGTCCTCAATGCACCTGTGGCTGTCGTTGCGGGGAACC
GGCCCAGTTACCTGTACAGGATGCTGTGCTCTCTACCCTCAGCCCAGGGGTTGTCTTCCCAAATGATAACAGTTTTCATC
GATGGCTACTATGAGGAACCGACTGCTGTGGTGGCTGCTGTTTGGTCCAAGGGGCATCCAGCACACTTCTTTCAGTGTCA
AGAATACCCTTGTGTCTCAGCACAACGAGGCCAGCCTCACTGCCACTTTCAACCTGTTTCCGGAAGCCAGGTTTGCTGTG
GTTCTGGAAGGAGGACCTGGACACTGCTGTGGATATTTTCAGTTTCCTGAGCCAATCCATCCAGCTGCTAGAGGAGGACG
ACAGCTTGTACTGGATCTCTCCCTGGAATGACCAGGGCTATGAGCACACAGCTGAGGACCCAGCACTGCTGTACCATATG
GAGACCATGCCTAGGCTGGGCTGGGTGCTCAGAAATCCTTGTACAAGGAGAAGCTTGAGCCCCAGGGGTCCACACTGGAA
AAGCTCTGGGCTTGGGATATGTGGATGCCAATGCTGGAACAATGCAAGGTACAGAGTGCAACATCCCTTATGTGTCCTGA
TCCTACCACTTGGGCATCATTGGCCTCAACATGAACAGCTGCTTCCATAAGGATTACTTCCGGAAGCACAATTCAACACA
GTTCCAGGTGTCCAGCTCAGGAACATGGACAGTCTGAAGAAGCACGCTTATGTAGTGGCAGTTCACAGGCTGCTCAATGA
AGCCAAGGTTCTCGACCACAGCAAGAACCCTTGTGAAGACTCTGTTCCTGCCAGGCACAGAGGGCCACACCTACACGGCC
TTTATCCGAATTGAGAAAGATGATGACTTCATCACCTGGACACAGCTTGTCAAGTGCCTCCATTATCTGGGACCTGGATG
TGCGTGGCAACCACCGGGGCCTATGGAGATTGTTTCAGAAAAAGAACCACTTCCTGGCGGTGGGTGTCTCTGCCTCTCCC
TACTCAATGAAGAAGCCACCATCAGTCTTCTTGGAGCCACCCCCAAAGAGGCAGGAGCCCCAGGAGCTGCAGAACAGACA
ORF - retro_btau_447 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.07 % |
| Parental protein coverage: | 76.82 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 9 |
Retrocopy - Parental Gene Alignment:
| Parental | PHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVLGE |
| PH.DE.MVLFLNM.APG....C..KD.GSFHLKDTAKALLR...SQAGPALGW..TWAFVG.KG.P.LGE | |
| Retrocopy | PHIDETMVLFLNMMAPGQGFTCIIKDTGSFHLKDTAKALLRRRDSQAGPALGWKETWAFVG*KGDPILGE |
| Parental | KHSKSPALSSWGDPVLLKTDVPLSSAEEAE---CHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFS |
| KHS.SPALSS.G..VLLKTDVPLSSAEEAE...CHWAD.ELN.....FCSK..G.G...SCKDPTP..FS | |
| Retrocopy | KHSDSPALSSCGGSVLLKTDVPLSSAEEAEMKMCHWADMELNHHSCCFCSKIKGDGNMYSCKDPTPSQFS |
| Parental | PD-PLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVA-LFGLRGIQH |
| PD.P.PDNKVLN.PVAV.AGNRP.YLYRML.SL.SAQG.S.QMITVFIDGYYEEP..VVA.LFG.RGIQH | |
| Retrocopy | PD<PTPDNKVLNAPVAVVAGNRPSYLYRMLCSLPSAQGLSSQMITVFIDGYYEEPTAVVA>LFGPRGIQH |
| Parental | TPISIKNARVSQHYKASLTATFNLFPEAKFAVVLE-EDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWND |
| T..S.KN..VSQH..ASLTATFNLFPEA.FAVVLE.EDLD.AVD.FSFLSQSI.LLEEDDSLY.IS.WND | |
| Retrocopy | TSFSVKNTLVSQHNEASLTATFNLFPEARFAVVLE>EDLDTAVDIFSFLSQSIQLLEEDDSLYWISPWND |
| Parental | QGYEHTAEDPALLYRVETMPGLGWVLR-KSLYKEELEPKWPTPEKLWDWDMWMRMPEQ-RRGRECIIPDV |
| QGYEHTAEDPALLY..ETMP.LGWVLR.KSLYKE.LEP...T.EKLW.WDMWM.M.EQ...G.EC.IP.V | |
| Retrocopy | QGYEHTAEDPALLYHMETMPRLGWVLR<KSLYKEKLEPQGSTLEKLWAWDMWMPMLEQ<MQGTECNIPYV |
| Parental | SRSYHFGIVGLNMNGYFHEAYFKKH-KFNTVPGVQLRNVDSLKKDAYEVEVHRLLSEAEVLDHSKNPCED |
| S.SYH.GI.GLNMN..FH..YF.KH..FNTVPGVQLRN.DSLKK.AY.V.VHRLL.EA.VLDHSKNPCED | |
| Retrocopy | S*SYHLGIIGLNMNSCFHKDYFRKH<QFNTVPGVQLRNMDSLKKHAYVVAVHRLLNEAKVLDHSKNPCED |
| Parental | S-FLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLR-IWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYS |
| S.FLP.TEGHTY.AFIR.EKDDDF.TWTQL.KCL..IWDLDVRGNHRGLWRLF.KKNHFL.VGV.ASPYS | |
| Retrocopy | S>FLPGTEGHTYTAFIRIEKDDDFITWTQLVKCLH>IWDLDVRGNHRGLWRLFQKKNHFLAVGVSASPYS |
| Parental | MKKPPSITPIFLESP-PKEEGGPGAAEQT |
| MKKPPS....FLE.P.PKE.G.PGAAEQT | |
| Retrocopy | MKKPPS---VFLEPP<PKEAGAPGAAEQT |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 11 .61 RPM |
| ERP005899_muscle | 0 .00 RPM | 45 .35 RPM |
| SRP017611_brain | 0 .05 RPM | 38 .32 RPM |
| SRP017611_kidney | 0 .00 RPM | 64 .43 RPM |
| SRP017611_liver | 0 .00 RPM | 21 .44 RPM |
| SRP030211_testis | 0 .27 RPM | 109 .22 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_447 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_447 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_447 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000013322 | 1 retrocopy |
retro_btau_447 ,
|
| Otolemur garnettii | ENSOGAG00000003522 | 2 retrocopies |