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 symbol: POMGNT1
• Ensembl ID: ENSBTAG00000013322
• Aliases: None
• Description: protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 [Source:RefSeq peptide;Acc:NP_001019656]

Sequence

>retro_btau_447
CCTCATATAGATGAGACCATGGTGCTGTTCCTCAACATGATGGCACCTGGCCAAGGGTTCACCTGCATTATTAAGGACAC
AGGCTCCTTCCATCTCAAGGACACAGCCAAGGCTCTGCTGAGGAGGCGCGACAGCCAGGCTGGCCCTGCCCTGGGCTGGA
AAGAGACCTGGGCCTTCGTGGGATGAAAAGGAGATCCTATCCTTGGGGAGAAACATTCTGACTCACCTGCCCTCTCCTCC
TGCGGGGGTTCAGTTCTGCTGAAGACAGATGTGCCACTAAGCTCAGCTGAAGAGGCAGAGATGAAGATGTGCCACTGGGC
AGACATGGAGCTGAACCATCACAGCTGCTGCTTCTGCAGCAAAATCAAGGGCGACGGGAACATGTACAGCTGCAAGGACC
CCACACCTTCCCAGTTCAGCCCTGACCCACCCCAGACAACAAGGTCCTCAATGCACCTGTGGCTGTCGTTGCGGGGAACC
GGCCCAGTTACCTGTACAGGATGCTGTGCTCTCTACCCTCAGCCCAGGGGTTGTCTTCCCAAATGATAACAGTTTTCATC
GATGGCTACTATGAGGAACCGACTGCTGTGGTGGCTGCTGTTTGGTCCAAGGGGCATCCAGCACACTTCTTTCAGTGTCA
AGAATACCCTTGTGTCTCAGCACAACGAGGCCAGCCTCACTGCCACTTTCAACCTGTTTCCGGAAGCCAGGTTTGCTGTG
GTTCTGGAAGGAGGACCTGGACACTGCTGTGGATATTTTCAGTTTCCTGAGCCAATCCATCCAGCTGCTAGAGGAGGACG
ACAGCTTGTACTGGATCTCTCCCTGGAATGACCAGGGCTATGAGCACACAGCTGAGGACCCAGCACTGCTGTACCATATG
GAGACCATGCCTAGGCTGGGCTGGGTGCTCAGAAATCCTTGTACAAGGAGAAGCTTGAGCCCCAGGGGTCCACACTGGAA
AAGCTCTGGGCTTGGGATATGTGGATGCCAATGCTGGAACAATGCAAGGTACAGAGTGCAACATCCCTTATGTGTCCTGA
TCCTACCACTTGGGCATCATTGGCCTCAACATGAACAGCTGCTTCCATAAGGATTACTTCCGGAAGCACAATTCAACACA
GTTCCAGGTGTCCAGCTCAGGAACATGGACAGTCTGAAGAAGCACGCTTATGTAGTGGCAGTTCACAGGCTGCTCAATGA
AGCCAAGGTTCTCGACCACAGCAAGAACCCTTGTGAAGACTCTGTTCCTGCCAGGCACAGAGGGCCACACCTACACGGCC
TTTATCCGAATTGAGAAAGATGATGACTTCATCACCTGGACACAGCTTGTCAAGTGCCTCCATTATCTGGGACCTGGATG
TGCGTGGCAACCACCGGGGCCTATGGAGATTGTTTCAGAAAAAGAACCACTTCCTGGCGGTGGGTGTCTCTGCCTCTCCC
TACTCAATGAAGAAGCCACCATCAGTCTTCTTGGAGCCACCCCCAAAGAGGCAGGAGCCCCAGGAGCTGCAGAACAGACA

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_447 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_447 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_447 has 0 orthologous retrocopies within eutheria group .

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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	retro_ogar_1864, retro_ogar_642,