RetrogeneDB ID: retro_btau_1492

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:52147500..52148866(-)
• Located in intron of: None

Retrocopy information

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

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_1492
ATGGGTGACCTGTGCTCGGACATCACCGAGGCCATGCTATATGAAAAGTTCAGTCCTGCGGGGCCTGTGCTGTCCATCTG
GGCCTGCCGTTATACGATCACCCGCCGCTCCCTGGGTTATGCCTACGTCAACTTCCAGCAGCCGGCCGACGCTGAGAGGG
CCTTGGACACCATGAACTTTTATGTAATTAAGGGAAAGCCGATCCGAATCATGTGGTCTCAGAGGGATCCGTCTCTGAGA
AAATCTGGTGTGGGAAACGTCTTCATCAAGAACCTGGACAACTCTATAGATGACAAGGCACTTTATGATACTTTTTCTGC
TTTTGGGAACATTCTGTCCTGCAAGGTGGTGTGTGATGAAAACGGTTCTAAGGTTTATGCCTTTATCCACTTTGAGACCC
AGGAGGCTGCCGACAAGGCCACTGAGAAGATGAACGGCATGCTCCTCAACGACCGTAAAATTTGTGGGCAGATTCAAGTC
TCGAAAAGAGCAGGAAGCTGAACTTGGAGCCAAAGCCAAGGAACTCAGCAATGTTTACATCAAAAACTTCGGGGAAAAGG
TTGATGATGAGAATCTGAAAGAGCTATTTAGCCAGTTTAGTAAGACCCTAAGTGTCAAGGTGATGAGAGATCCCAGTGGG
AAATCCAAAGGCTTTGACTTTGTGAGTTATGAAAAACACGAGGATGCCAATAAGGCTGTGGAAGAGATGAATGGAAAAGA
AATCACTGGGAAGGTCATTTTCGTTGGCTGTGCACAAAAGAAAGTGGAGTGGCAGGCCGAGTTAAAGCGAAAATTTGAAC
AGCTGAAGCAGGGGAGGATTAGTCACTATCAGGGGGTGAATCTCTACATTTAAAACTTGGATGAAACCATCGATGACAAG
AAGTTAAGGAAAGAGTTTTCTCCTTTTGGATCAATCGCCAGTGCTAAGGTGATGCTGGAGGATGGGAGAAGCAAAGGATT
TGGCTTTGTCTGCTTCTCGTCCCCTGAAGAGGCAACCAAAGCAGTCACAGAGATGAATGGATGCATCGTGGGCTCCAAGC
CACTGTATGTCGCTCTGGCCCAGAGAAAGGAGGAGAGAAAGGCTCACCTGACCAACCAGTATATGCAGCAGGTGGCTGGG
ATGAGGGCACTGCCCACCAATGCCATCTTAAATCAGTTCCTGCCTGCAGCTGGGGGCTACTTTGTGCCAGCAGTTCCACA
GACTCAGGGATGACCTCTGTATTACACACCTAACCAGTTAGCACAGATGAGGTCTAATCCACACTTGCAGCAAGGTGAGA
GACCTCAAGGCTTCCAAGGAATGCCAAGTGCTATACACCAGTCTGGGCCTCGTCCAGCTCTTTGCCATCTGGCTCCAACT
GGTAAT

Alignment

ORF - retro_btau_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.06 %
• Parental protein coverage: 70.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPIRI
          .GDL.SD.TEAMLYEKFSPAGPVLSI..CR..ITRRSLGYAYVNFQQPADAERALDTMNF.VIKGKPIRI
Retrocopy MGDLCSDITEAMLYEKFSPAGPVLSIWACRYTITRRSLGYAYVNFQQPADAERALDTMNFYVIKGKPIRI

Parental  MWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFETQEAADKA
          MWSQRDPSLRKSGVGNVFIKNLD.SID.KALYDTFSAFGNILSCKVVCDENGSK.YAF.HFETQEAADKA
Retrocopy MWSQRDPSLRKSGVGNVFIKNLDNSIDDKALYDTFSAFGNILSCKVVCDENGSKVYAFIHFETQEAADKA

Parental  IEKMNGMLLNDRKVFVGRFKSRK-EREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQFGKTLSVKVM
          .EKMNGMLLNDRK...G.....K.E.EAELGAKAKE..NVYIKNFGE.VDDENLKELFSQF.KTLSVKVM
Retrocopy TEKMNGMLLNDRKI-CGQIQVSK>EQEAELGAKAKELSNVYIKNFGEKVDDENLKELFSQFSKTLSVKVM

Parental  RDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEITGKVIFVGRAQKKVERQAELKRKFEQLKQERISRYQG
          RDPSGKSKGF.FVSYEKHEDANKAVEEMNGKEITGKVIFVG.AQKKVE.QAELKRKFEQLKQ.RIS.YQG
Retrocopy RDPSGKSKGFDFVSYEKHEDANKAVEEMNGKEITGKVIFVGCAQKKVEWQAELKRKFEQLKQGRISHYQG

Parental  VNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGRIVGSKPL
          VNLYI.NLD.TIDD.KLRKEFSPFGSI.SAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNG.IVGSKPL
Retrocopy VNLYI*NLDETIDDKKLRKEFSPFGSIASAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGCIVGSKPL

Parental  YVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPAAGGYFVPAVPQAQGRPPYYTPNQLAQMRP
          YVALAQRKEERKAHLTNQYMQ.VAGMRALP.NAILNQF.PAAGGYFVPAVPQ.QG.P.YYTPNQLAQMR.
Retrocopy YVALAQRKEERKAHLTNQYMQQVAGMRALPTNAILNQFLPAAGGYFVPAVPQTQG*PLYYTPNQLAQMRS

Parental  NPRWQQGGRPQGFQGMPSAIRQSGPRPALRHLAPTGS
          NP..QQG.RPQGFQGMPSAI.QSGPRPAL.HLAPTG.
Retrocopy NPHLQQGERPQGFQGMPSAIHQSGPRPALCHLAPTGN

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	36.70 RPM
ERP005899_muscle	0.05 RPM	90.74 RPM
SRP017611_brain	0.00 RPM	36.27 RPM
SRP017611_kidney	0.00 RPM	74.92 RPM
SRP017611_liver	0.00 RPM	54.59 RPM
SRP030211_testis	0.05 RPM	208.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1492 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1492 has 0 orthologous retrocopies within eutheria group .

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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,