RetrogeneDB ID: retro_ocun_642

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:32506885..32507938(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022552
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSOCUG00000026859
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_ocun_642
GAGAAAACTTTAGAAACTGTTCCTTTGGAGAGGAAAAAGAGAGAAAAGGAACAGTTCCGTAAACTCTTTATTGGGGGCTT
AAGCTTTGAAACCACAGAAGAAAGTTTGAGGAACTACTACGAACAATGGGGAAAACTTACAGATTGTGTGGTGATGAGGG
ATCCTGCAAGCAAAAGATCAAGAGGATTTGGTTTTGTTACTTTCTCATCCATGGCTGAGGTTGATGCTGCCATGGCTGCA
AGACCTCACTCAATTGATGGGAGAGTGGTTGAGCCAAAGCGTGCTGTAGCAAGAGAAGAATCTGGAAAACCTGGGGCTCA
TGTAACTGTGAAGAAGCTGTTTGTTGGTGGAATTAAAGAAGATACTGAGGAACATCACCTTAGAGATTACTTTGAAGAAT
ATGGAAAAATTGATACCATTGAAATAATTACTGATAGGCAGTCTGGGAAGAAAAGAGGCTTTGGCTTTGTTACTTTTGAT
GACCATGATCCTGTGGATAAAATTGTATTGCAAAAGTACCACACCATCAATGGTCATAATGCAGAAGTAAGAAAGGCTTT
GTCTAGACAAGAAATGCAAGAAGTCCAGAGTTCTAGGAGTGGAAGAGGAGGTAACTTTGGTTTTGGAGATTCACGTGGTG
GTGGTGGGAATTTTGGACCAGGGCCAGGAAGTAATTTTAGAGGATCTGATGGATATGGAAGTGGACGTGGATTTGGAGAT
GGCTATAATGGGTATGGAGGAGGACCTGGAGGTGGCAATTTTGGAGGTAGCCCTGGTTATGGAGGAGGAAGAGGAGGATA
TGGTGGTGGAGGACCTGGATATGGCAACCAGGGTGGGGGCTACGGAGGTGGTTATGACAACTATGGAGGAGGAAATTACG
GAAGTGGAAATTATAATGATTTTGGAAATTACAACCAGCAACCCTCTAACTACGGTCCAATGAAGAGTGGAAACTTTGGT
GGTAGCAGAAACATGGGGGGACCATATGGTGGAGGAAACTATGGTCCAGGAGGCAGTGGAGGAAGTGGGGGTTATGGTGG
GAGGAGCCGATAT

Alignment

ORF - retro_ocun_642 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.43 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS
          .KTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS
Retrocopy EKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS

Parental  MAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTI
          MAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTI
Retrocopy MAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTI

Parental  EIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGD
          EIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGD
Retrocopy EIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGD

Parental  SRGGGGNFGPGPGSNFRGSADGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGG
          SRGGGGNFGPGPGSNFRGS.DGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGG
Retrocopy SRGGGGNFGPGPGSNFRGS-DGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGG

Parental  GYGGGYDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRS
          GYGGGYDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRS
Retrocopy GYGGGYDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRS

Parental  RY
          RY
Retrocopy RY

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
SRP017611_brain	33.39 RPM	108.28 RPM
SRP017611_kidney	39.12 RPM	109.67 RPM
SRP017611_liver	15.95 RPM	57.73 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_642 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_642 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_642 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
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	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
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,