RetrogeneDB ID: retro_itri_717

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393313.1:12298683..12299620(-)
• Located in intron of: ENSSTOG00000023589

Retrocopy information

• Ensembl ID: ENSSTOG00000026412
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSSTOG00000006202
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_itri_717
GAGAGAGAAAAGGTACAGTTCCGTAAACTCTTTATTGGTGGCTTAAGTTTTGAAACCACAGAGGACAGTTTAAGAAACTA
CTACGAGCAATGGGGAACACTTACAGATTGTGTGGTTATGAGGGATCTTGCAAGCAAAAGATCAAGAGGATTTGGTTTTG
TAACTTTCTCATCCATGGCTGAGGTTGATGTTGCCATGGCTGCGAGACCTCATTCCATCGATGGGAGAGTGGTAGAGCCA
AAACGAGCTGTAGCAAGAGAGGAATCTGGAAAACCAGGGGCTCGTGTGACTGTGAAGAAGCTGTTTTTTTGGCGGAATTA
AAGAAGATCCCGAGGAACACCACCTTAGAGATTACTTTGAAGAATATGGAAAAATCGACACCATTGAGATAATTACTGAT
AGACAGTCTGGAAAGAAAAGAGGCTTTGGTTTTGTGACTTTTGATGACCATGATCCTGTGGACAAAATTGTATTGCAAAA
ATACCACACCATCAATGGTCATAATGCAGAAGTAAGAAAGGCTTTGTCTAGACAAGAAATGCAAAAAGTCCAAAGTTCCA
AGAGTGGAAGAGGAGGCAACTTTATAGGAAGATCTGATGGATATGGAAGTGGACGTGAATTTGGGGGTGGCTCTAATGGA
TCTGGAGGAGGACCTGGACATGGCAATTTTGGAGGTAGCTCTGGTTATCGAGGAGGAAGAGGAGGCTATGGTGGTAGAGG
ATCTGGCTATGGAAACCGGGGTGGGGGCTATGGAGGTGGTTATGATAACTATGGAGGAGGAAATCATGGAAGTGGAATTT
ATAATGATTTTGGAAATTATAACCAGCAACCTTCTAAATATAGTCTAATGAAGAGTGGAAACTTGGGTAGCAGGAACATG
GGGCGAGCACGTGGTAGAGGAAATGATGGTCCTGGAGGAAGTGAGGGTTATGGTGGG

Alignment

ORF - retro_itri_717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 89.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARP
          .REK.QFRKLFIGGLSFETTE.SLRNYYEQWG.LTDCVVMRD.ASKRSRGFGFVTFSSMAEVD.AMAARP
Retrocopy EREKVQFRKLFIGGLSFETTEDSLRNYYEQWGTLTDCVVMRDLASKRSRGFGFVTFSSMAEVDVAMAARP

Parental  HSIDGRVVEPKRAVAREESGKPGAHVTVKKLFV-GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKK
          HSIDGRVVEPKRAVAREESGKPGA.VTVKKLF..GGIKED.EEHHLRDYFEEYGKIDTIEIITDRQSGKK
Retrocopy HSIDGRVVEPKRAVAREESGKPGARVTVKKLFF>GGIKEDPEEHHLRDYFEEYGKIDTIEIITDRQSGKK

Parental  RGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNF-GFGDSRGGGGNFGP
          RGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQ.VQSS.SGRGGNF.G..D..G.G..F..
Retrocopy RGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQKVQSSKSGRGGNFIGRSDGYGSGREF--

Parental  GPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGG-YDNY
          G.GSN..GG..G.G....FG.G..GY.GG.GG....GS.GYG...GGYGGG...YG..GG..G.G.Y...
Retrocopy GGGSNGSGGGPGHGN---FG-GSSGYRGGRGGYGGRGS-GYGNRGGGYGGGYDNYG--GGNHGSGIYNDF

Parental  GGGNYGSGSYNDFGNYNQQPSNYGPMKS-GNF--GGSRNMGG
          G..N.....Y......N....N.G.....GN...GGS...GG
Retrocopy GNYNQQPSKYSLMKSGNLGSRNMGRARGRGNDGPGGSEGYGG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_717 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_717 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 53 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	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 ,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,