RetrogeneDB ID: retro_opri_165

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3156:116516..117196(-)
• Located in intron of: ENSOPRG00000009867

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSOPRG00000011698
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_opri_165
GAAGGCACTGAGGAACTTCACCTTAGAGATTACTTTGAAGAATAGGGGACAAATTATTATTGAAATAATCACTGATAGGC
AATCTGGAAAGAAAAGAGGCTGTAGCTTTGTTGCTTTTGATGATCTTGATCCTCTGGATTAAATTGTGTTGCAAGAATAC
CATATTATCAATGGTCATAATGCAGAAGTAAGAAAGGCTTTGTCTAGGAAGTTCAAAAGTTCTAGGAGTAGAGGAAGAGG
TAACTTTGGTTTTGGAGATTCATGTGGTGATGGTGGAAATTTTGGACCAGAAGCAGGAAGTAATTTTAGATCTGGTGGAT
ATGGAAGTGAATGTGGATTTGGAGATGGCTATTACAGGTATGGAAGAAGACCTGAAGGTGGTAATTTTGGAGGTAGCCCT
GGTTTTGGAGGAGGAGAAGGAGGAGAAGGGGCTGGAAGACTTGGATAGGCAGCCAGGATGGGGGCTACAAAGGTGCAGTG
TTATAACACCAATAGAGGAAGAAATTATGGAAGTGGAAATTACAATGATTTGGGAAATTATAACCAACAATCTTCTAACT
ACAGCCCGATGAATAGTGGAAACATTGGTCATAGCAGGACATGGGGGACTGTATGGTGGAAGAATTTATGGTCCAGGTGG
CACTAGAAGAAGTGGGGGGGATGGTGGGAGGAGCTGATAT

Alignment

ORF - retro_opri_165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.39 %
• Parental protein coverage: 58.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EDTEEHHLRDYFEE-YGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALS
          E.TEE.HLRDYFEE..G.I..IEIITDRQSGKKRG..FV.FDD.DP.D.IVLQ.YH.INGHNAEVRKALS
Retrocopy EGTEELHLRDYFEE>RGQI-IIEIITDRQSGKKRGCSFVAFDDLDPLD*IVLQEYHIINGHNAEVRKALS

Parental  RQEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPGPGSNFRGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSP
          R.......SSRS...GNFGFGDS.G.GGNFGP..GSNFR.S.GYGS..GFGDGY..YG..P.GGNFGGSP
Retrocopy RK----FKSSRSRGRGNFGFGDSCGDGGNFGPEAGSNFR-SGGYGSECGFGDGYYRYGRRPEGGNFGGSP

Parental  GYGGGRGGYGGGGPG-YGSQ-GGGYGGG-YDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSR-N
          G..........G..G..GSQ.GG..G...Y....G.NYGSGNYND.GNYNQQ.SNY.PM.SGN.G.SR..
Retrocopy GFXXXXXXXXAGRLG<IGSQDGGYKGAV>YNTNRGRNYGSGNYNDLGNYNQQSSNYSPMNSGNIGHSR<D

Parental  MG-GPYGGGNYGPGGSGGSGGYGGRSRY
          MG.G.YGG..YGPGG...SGG.GGRS.Y
Retrocopy MG<GLYGGRIYGPGGTRRSGGDGGRS*Y

Legend:

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

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_165 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps 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 21 parental genes, and 61 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,
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041,
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,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Ochotona princeps	ENSOPRG00000006107	10 retrocopies	retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165 , retro_opri_893,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339,
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,