RetrogeneDB ID: retro_btau_656

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:24418850..24420067(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000046902
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSBTAG00000017125
• Aliases: None
• Description: polyadenylate-binding protein 4 [Source:RefSeq peptide;Acc:NP_001077193]

Sequence

>retro_btau_656
GCAGCCAAGTACCGCCAGGCCTCCCTGTACGTAGGTGACCTCCATGCGGATGTCACCGAGGACCTGCTGTTCAAGAAGTT
CAGCGCCGTGGGCCCCGTGTTGTCCATCCGCATCTGCAGGGACCTGGTCACCCGCCGCTCCCTGGGCTACGCCTATGTGA
ACTTTCTGCAGCTGGCGGATGCCCAAAAGGCCCTGGACACCATGAACTTTGACCTGATAAAGGGCAAATCCATCCGTCTC
ATGTGGTCTCAACGTGACGCCTACTTAAGGAAATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAGATCCATTGA
TAACAAAACCCTTTATGAACACTTTTCAGCGTTTGGGAAGATCCTGTCCTCCAAGGTGATGAGTGATGATCACGGCTCCC
GGGGCTATGCATTCGTGCACTTTCAAAACCAGATTGCTGCAGACAGGGCCATCGAGGAGATGAATGGGGCACTGCTTAAG
GACTGCAGGCTGTTTGTTGGCAGATTCAAAAGCCGCAAAGATCGAGAAGCCGAGTTTCAAAACAAAGCCCATGAATTCAC
CAATGTTTACATCAAAAATTTCGGAGATGAGATGGATGATGAGAGACTAAAGGAAGTTTTCAGCAAGTACGGCAAAACCC
TGAGTGTTAAGGTTATGACAGATTCCAGTGGAAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCACGAGGCTGCC
AAAAGGGCTGTTGAAGAAATGAATGGAAAGGACATAAACGGACAGCTGCTTTTTGTAGGCCGGGCACAGAAGAAAGCAGA
GCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAACATGAAAGATTTCGGCGGTGCCAGGGTGCGAAGCTCTATA
TTAAGAACCTGGATGAGACCATTGATGATGAAAAACTGCGGAGGGAATTTTCTTCATTTGGATCAATTAGCAGGGTTAAG
GTAATGCAGGAAGAAGGGCGAAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTGCGGAGGAGGCCACTAAAGCAATGAC
GGAGATGAATGGCCGCATCTTAGGCTCCAAGCCACTCAACATCGCCCTGGCCCAGAAACCCTAGGAGAGGAAAACTTTCT
GCATCAGCCAGTGTGTGCTGCAGACTAAGAAATGTTAGTGATCTCTGCCTGAATTCTCCTCAGTCAATTTTAAATTCCAG
CTGATGGCTGGTTAGTT

Alignment

ORF - retro_btau_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.78 %
• Parental protein coverage: 62.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF
          A..Y..ASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALDTMNF
Retrocopy AAKYRQASLYVGDLHADVTEDLLFKKFSAVGPVLSIRICRDLVTRRSLGYAYVNFLQLADAQKALDTMNF

Parental  DVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVH
          D.IKGK.IR.MWSQRD..LRKSG.GNVFIKNLD.SIDNK.LY..FSAFG.ILS.KV..D..GS.GYAFVH
Retrocopy DLIKGKSIRLMWSQRDAYLRKSGIGNVFIKNLDRSIDNKTLYEHFSAFGKILSSKVMSDDHGSRGYAFVH

Parental  FETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQF
          F..Q.AAD.AIE.MNG.LL.D...FVGRFKSRK.REAE...KA.EFTNVYIKNFG.E.DDE.LKE.FS..
Retrocopy FQNQIAADRAIEEMNGALLKDCRLFVGRFKSRKDREAEFQNKAHEFTNVYIKNFGDEMDDERLKEVFSKY

Parental  GKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEITGKVIFVGRAQKKVERQAELKRKFEQLK
          GKTLSVKVM.D.SGKSKGFGFVS...HE.A..AVEEMNGK.I.G...FVGRAQKK.ERQAELK..FEQLK
Retrocopy GKTLSVKVMTDSSGKSKGFGFVSFDSHEAAKRAVEEMNGKDINGQLLFVGRAQKKAERQAELKQMFEQLK

Parental  QERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMN
          .ER..R.QG..LYIKNLD.TIDDEKLR.EFS.FGSI...KVM.E.GRSKGFG..CFSS.EEATKA.TEMN
Retrocopy HERFRRCQGAKLYIKNLDETIDDEKLRREFSSFGSISRVKVMQEEGRSKGFGLICFSSAEEATKAMTEMN

Parental  GRIVGSKPLYVALAQRKEERKAHLTNQYMQRVA-GMRALPANAILNQFQPAAGGYFV
          GRI.GSKPL..ALAQ...ERK.....Q........M....A...L.QF...A.G..V
Retrocopy GRILGSKPLNIALAQKP*ERKTFCISQCVLQTK<EMLVISA*ILLSQF*IPADGWLV

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	0.07 RPM	36.70 RPM
ERP005899_muscle	0.37 RPM	90.74 RPM
SRP017611_brain	0.46 RPM	36.27 RPM
SRP017611_kidney	2.07 RPM	74.92 RPM
SRP017611_liver	0.23 RPM	54.59 RPM
SRP030211_testis	0.37 RPM	208.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_656 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BM031131	24418768	24419305	100	536	0	536

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_656 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_502
Oryctolagus cuniculus	retro_ocun_792

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656 ,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,