RetrogeneDB ID: retro_btau_1330

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:94002829..94003420(+)
• Located in intron of: ENSBTAG00000001754

Retrocopy information

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

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_1330
AGATCAAGAGGATTTGGTTTTGTGACTTTTTCTTCCATGGCTGAAGTTGATGCTGCCATGGCTGCAAGACCTCATTCAAT
TGATGGGAGAGTGGTTGAGCCAAAACGTGCTGTTGCAAGAGAGGAATCTGGAAAGCCGGGGGCTCATGTAACTGTGAAGA
AGCTGTTTGTTGGTGGAATTAAGGAAGATACTGAGGAACATCATCTTAGAGATTACTTTGAGGAATATGGAAAAATTGAT
ACCATTGAGATTATTACTGACAGGCAGTCTGGAAAGAAAAGAGGCTTTGGATTTGTTACTTTTGATGACCATGATCCTGT
GGATAAGATTGTGTTGCAAAAATACCATACTGTCAATGTTCATAATGCAGAAGTAAGAAAGGCTTTGTCTAGACAAGAAA
TGCAGGAAGTCCAAAGTTCTAGAAGTGGAAGAGGAGGCAACTTTGGTTTTGGAGATTCTCGTGGTGGCGGTGGGAATTTT
GGACCAGGACCAGGAAGTAACTTTAGAGGAGGATCTGATGGATATGGAAGTGGCCGTGGATTTGGGGATGGCTATAATGG
GTATGGAGGAGGACCTGGAGGTGGCAATTTT

Alignment

ORF - retro_btau_1330 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.98 %
• Parental protein coverage: 57.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLR
          RSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLR
Retrocopy RSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLR

Parental  DYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSS
          DYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHT.N.HNAEVRKALSRQEMQEVQSS
Retrocopy DYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTVNVHNAEVRKALSRQEMQEVQSS

Parental  RSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNF
          RSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNF
Retrocopy RSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNF

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	0.29 RPM	258.18 RPM
ERP005899_muscle	1.95 RPM	291.24 RPM
SRP017611_brain	2.24 RPM	456.29 RPM
SRP017611_kidney	1.07 RPM	497.29 RPM
SRP017611_liver	1.13 RPM	221.99 RPM
SRP030211_testis	3.71 RPM	451.98 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1330 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1330 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,