RetrogeneDB ID: retro_btau_1535

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:43551338..43552134(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020849
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSBTAG00000005726
• Aliases: HNRNPA2B1, HNRPA2B1
• Description: Heterogeneous nuclear ribonucleoproteins A2/B1 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJ60]

Sequence

>retro_btau_1535
AAGAAGGAACAAGAACAATTCCGTAAACTCTTTATTGGTGGCTTGAGCTCTGAAACCACAGAAGAAAGTCTGAGGAACTA
CTACAAGCAGTGGGGAAAGCTTATAAGCTGTGAGATCATAAGGGACCATGCAAGCAAAAGATCAAGAGGGTTTGGTTTTG
TCACCTTTTCATCCATGGCTGAAGTGGATGCTGCCATGGCTGCCAGACCTCACTCTATTGATGGGAAAACAATTGCCCCC
AAACGTGCTGTCCCAAGAGAGGAATCTGGACAGCGAGGGGTTTTCCTAACTGTGAAGAAGCTGTTTGTTGGTGGAATTGA
AGATACCGAGGAACATCATCTTAGATATTACTTTGAGAAATATGGAAAAATCGATGCCATTGAGATAATTACTGATAGAG
AGTCTGGAAGAAAAAGAGGCTTTGGATTTGTGACTTTTGATGACCATGATCCCGTGGATAAGATTGTGTTGCAGAAAAAC
CATATCATCAATGGCCATCAGGCAGAAGTAAGAAAGGCCTTTTCTCGACCTAAAATGCAACAAGTCCAGCATTCTAGAAG
TAGAAGGGGAGACAACGCTGGTTTTGGAGATTCTCCTGGTGATGATGGAAATGTTGGACCAGGGTCAAGACGAGGAAGTA
GCTTTGGAGGACGATCTGATGGATTGAGAAGCGGTCAGTGGACTTGGTCATGGTTATAATAGGTGTGGAGAATGACCAGG
AAGTGGCAATTTGGGAGTTAGCCCTGGTTATGAAGGAGGAAAAGGAGCTTATGGTGGTGGACAACTTGGATATGGA

Alignment

ORF - retro_btau_1535 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 77.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP
          ..E.EQFRKLFIGGLS.ETTEESLRNYY.QWGKL..C...RD.ASKRSRGFGFVTFSSMAEVDAAMAARP
Retrocopy KKEQEQFRKLFIGGLSSETTEESLRNYYKQWGKLISCEIIRDHASKRSRGFGFVTFSSMAEVDAAMAARP

Parental  HSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKR
          HSIDG....PKRAV.REESG..G...TVKKLFVGGI.EDTEEHHLR.YFE.YGKID.IEIITDR.SG.KR
Retrocopy HSIDGKTIAPKRAVPREESGQRGVFLTVKKLFVGGI-EDTEEHHLRYYFEKYGKIDAIEIITDRESGRKR

Parental  GFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPGP
          GFGFVTFDDHDPVDKIVLQK.H.INGH.AEVRKA.SR..MQ.VQ.SRS.RG.N.GFGDS.G..GN.GPG.
Retrocopy GFGFVTFDDHDPVDKIVLQKNHIINGHQAEVRKAFSRPKMQQVQHSRSRRGDNAGFGDSPGDDGNVGPGS

Parental  --GSNFRGGSDGYGSGR-GFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYG
          ..GS.F.G.SDG..SG..G.G.GYN..G..PG.GN.G.SPGY.GG.G.YGGG..GYG
Retrocopy RRGSSFGGRSDGLRSGQ>GLGHGYNRCGE*PGSGNLGVSPGYEGGKGAYGGGQLGYG

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	258.18 RPM
ERP005899_muscle	0.00 RPM	291.24 RPM
SRP017611_brain	0.00 RPM	456.29 RPM
SRP017611_kidney	0.00 RPM	497.29 RPM
SRP017611_liver	0.00 RPM	221.99 RPM
SRP030211_testis	0.01 RPM	451.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1535 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1535 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1535 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001553	20 retrocopies	retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535 , retro_btau_193, retro_btau_228,
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Choloepus hoffmanni	ENSCHOG00000013832	15 retrocopies	retro_chof_1060, retro_chof_1191, retro_chof_1413, retro_chof_1460, retro_chof_1507, retro_chof_2062, retro_chof_2135, retro_chof_2235, retro_chof_2263, retro_chof_2404, retro_chof_2425, retro_chof_2473, retro_chof_2574, retro_chof_499, retro_chof_853,
Ciona intestinalis	ENSCING00000004062	1 retrocopy	retro_cint_7,
Ciona savignyi	ENSCSAVG00000000472	1 retrocopy	retro_csav_26,
Dasypus novemcinctus	ENSDNOG00000012928	1 retrocopy	retro_dnov_1978,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Felis catus	ENSFCAG00000027765	1 retrocopy	retro_fcat_692,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Mus musculus	ENSMUSG00000004980	1 retrocopy	retro_mmus_573,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,