RetrogeneDB ID: retro_btau_1842

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:100195783..100196947(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: KPNA3
• Ensembl ID: ENSBTAG00000004850
• Aliases: None
• Description: importin subunit alpha-3 [Source:RefSeq peptide;Acc:NP_001179702]

Sequence

>retro_btau_1842
ATGTGAAGATACAGAAATGAAATGACTGTTCAACTGCAAAAGAACAAAAGAGATGAACAATTACTGAAAAAAGAAATGTT
CCCCAAGAAAAAATTTAGAAGATTCAGATGCTGATTCTGATTTTAAAGCACACAATATAATACTAGAAACTATAATGCAG
AATGCTACAAGTGATAAATACCCAGTGGCCCAGTTGAGTGCTATACAGGCTGCAAGAAAACTTTTATCCAGTGACAGAAA
TCCACCAGGTGATGATCTAATAAAACCTTGGATTTTACCAATTCTAGTGAAGTGTCTAGAAAGGGATGATAATCCTTCAT
TACAGTTTGAAGCTGTATAAGTGTTAACTAATATAGCATCAGGAAGTTCTGCATAGACTCAAACTATTATACAGTTTAAT
ACTGTACCTCTTTTTCTAAGACTTCTCCTTTCAGCCACATCAGAATGTTTGTAAGCAAGCAGTATGGGCTTTGGGGAATA
TTGCAGGTGATGATCCTCAGAGTAGAGATTATGTCATGTTCACTGAGAGTTGTCAAAATTATTCTGTCTTTTATCAGTCC
CTCCATTCTTATTGCCCTCTTTTGGAATGTCTCATGGATTATTTTCAGTCTCTGCAGAAATAAGGACCGATTCCATCACC
TATGGAGACAGTCTGGAGATTTTGCCAGCATTGTGTGTCTTAATATATCATATGGACATGAACACTCTTGTGAATACTGT
TTGGGTGCTGTCACATCTGATAGATGGAATTAAAGAGCAGATACAGATGGTTATTGATTCAAGGGCTGTGCCATTTCTTT
TGTCCCTTCTGAGCCATCAGGAAATGAAAGTTCAAACAGCAGCACTGAGAGCAGTTGGCAACACAGTGACAGGTGCCAAC
GAGCAGACCCAGGTTGTTCTCAACTGCAATGTCCTGTCACACTTCCCAAATTTCTTATCACATCCAAAGAAGAAGATAAA
TAAGGAAGCAGTGTGATTCCTTTCCAACATTACAGCAGGCAACCAGCAACAAGTTCAAGCTGTAATAGATGTTGGATTAA
TCCTATGATTATTTATCAGCTTGCTAAGGGGGACTTTGGAACACAAAAGGGAGCTTTGGGGGCAATTAGCAACTTAATGA
TAAGTGGCAAAAAATATCAAGTTGAGTACTTTGTACAGCACAAT

Alignment

ORF - retro_btau_1842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 77.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MRRHRNEVTVELRKNKRDEHLLKK-RNVPQEE-SLEDSDVDADFKAQNVTLEAILQNATSDN-PVVQLSA
          M.R.RNE.TV.L.KNKRDE.LLKK.RNVPQE...LEDSD.D.DFKA.N..LE.I.QNATSD..PV.QLSA
Retrocopy M*RYRNEMTVQLQKNKRDEQLLKK<RNVPQEK<NLEDSDADSDFKAHNIILETIMQNATSDKYPVAQLSA

Parental  VQAARKLLSSDRNPPIDDLIKSGILPILVKCLERDDNPSLQFEAAWALTNIASGTSAQTQAVVQSNAVPL
          .QAARKLLSSDRNPP.DDLIK..ILPILVKCLERDDNPSLQFEA...LTNIASG.SA.TQ...Q.N.VPL
Retrocopy IQAARKLLSSDRNPPGDDLIKPWILPILVKCLERDDNPSLQFEAV*VLTNIASGSSA*TQTIIQFNTVPL

Parental  FLRLLHS-PHQNVCEQAVWALGNIIGDGPQCRDYVI-SLGVVKPLLSFINPSIPITFLRNVTWVIVNLCR
          FLRLL.S.PHQNVC.QAVWALGNI.GD.PQ.RDYV..SL.VVK..LSFI.PSI.I....NV.W.I..LCR
Retrocopy FLRLLLS>PHQNVCKQAVWALGNIAGDDPQSRDYVM>SLRVVKIILSFISPSILIALFWNVSWIIFSLCR

Parental  NKD-PPP-PMETV-QEILPALCVLIYHTDINILVDTVWALSYLTDGGNEQIQMVIDSGVVPFLVPLLSHQ
          NKD.P.P.PMETV..EILPALCVLIYH.D.N.LV.TVW.LS.L.DG..EQIQMVIDS..VPFL..LLSHQ
Retrocopy NKD<PIPSPMETV<LEILPALCVLIYHMDMNTLVNTVWVLSHLIDGIKEQIQMVIDSRAVPFLLSLLSHQ

Parental  EVKVQTAALRAVGNIVTGTDEQTQVVLNCDVLSHFPNLLSHPKEKINKEAVWFLSNITAGNQQQVQAVID
          E.KVQTAALRAVGN.VTG..EQTQVVLNC.VLSHFPN.LSHPK.KINKEAV.FLSNITAGNQQQVQAVID
Retrocopy EMKVQTAALRAVGNTVTGANEQTQVVLNCNVLSHFPNFLSHPKKKINKEAV*FLSNITAGNQQQVQAVID

Parental  AGLI-PMIIHQLAKGDFGTQKEAAWAISNLTISGRKDQVEYLVQQN
          .GLI.PMII.QLAKGDFGTQK.A..AISNL.ISG.K.QVEY.VQ.N
Retrocopy VGLI<PMIIYQLAKGDFGTQKGALGAISNLMISGKKYQVEYFVQHN

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	3.32 RPM
ERP005899_muscle	0.00 RPM	9.34 RPM
SRP017611_brain	0.00 RPM	17.27 RPM
SRP017611_kidney	0.00 RPM	12.39 RPM
SRP017611_liver	0.00 RPM	8.61 RPM
SRP030211_testis	0.00 RPM	10.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1842 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1842 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004850	1 retrocopy	retro_btau_1842 ,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Rattus norvegicus	ENSRNOG00000014945	1 retrocopy	retro_rnor_987,
Ictidomys tridecemlineatus	ENSSTOG00000003006	1 retrocopy	retro_itri_1777,
Tarsius syrichta	ENSTSYG00000008134	1 retrocopy	retro_tsyr_1547,