RetrogeneDB ID: retro_ogar_3077

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873711.1:1358467..1359401(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000034129
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA2B1
• Ensembl ID: ENSOGAG00000015353
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A2/B1 [Source:HGNC Symbol;Acc:5033]

Sequence

>retro_ogar_3077
AAAGAGCTTGAACAGCTGCAGAAGCTCTTCATTGGAGGGTTGAGCTTTGAAACGACTGATGAGAGTCTGAGGAACCATTC
TGAACAATGGGGAAAGCTCACAGACTGAGTGGTATGAGAGATCCAAACACCAAGCCCTCCAGGGGCTTTGGGTTTGTCAC
ATACACGACCCTGGAGGAGGTGGATGCAGCAATGAATGCAAGGCCACACAAAGTGGATGGAAGAGTTGTGGAACCAAAGA
GAGCTGTTTCCAGAGAAAATCCTCAAAGACCTGGTGCCCACTTAATTGTGAAAAAGATCTTTGCTGGTGGCATTAAAGAA
GAGACTGAAGAACATCACTTTAGAGACTGTTTTGAACAGTATGGGAAAATGGAAGTGATTGAAATCATGACTGACCGAGG
CAGTGATGAGAAGCGGGGATTTGCTTTTGTTACATTTGATGACCATGATTTTGTGGATAAGATTGTCATTCAGAAATACC
ATACTGTGAATGGCCACAACTGTGAAGTAAGGAAAGCCCTATCAAAGCAAGAGATGGCTAATGCTTCATTCAGCCAGAGG
TCAAAGTGGTTCTGGAAACTTTGGTGGGGGTCGTGGAGGTGGTTTTGGTGGAAATGACAATTTTGGCTGTGGAGGAAACT
TCAGTGGTTGTGGTGGCTTTGGTGGCAGCTGTGGTGGTGGTGGATATGGTAGCAGTGGGGATGGCTACAATGGATTTGGT
AACGATGGAAGCAATTTTCGAGGTGGTGGAAGTTACAATGATTTTGGCAATTACAACAATCAGTCATCAAATTTTGGACC
CATGAAGGGAGGAAATTTTGGAGGCAAAAGCTCTGGCCCTTATGGTGGTGGTGGTGGCCAATACTTTGCCAAACCACAAA
ACCAAGGTAGCTAATGGTGGTTCCAGTAGCAGCAGTAGCTATGGCAGTGGTAGA

Alignment

ORF - retro_ogar_3077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 88.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV-MRDPASKRSRGFGFVTFSSMAEVDAAMAARP
          .E.EQ..KLFIGGLSFETT.ESLRN..EQWGKLTD.VV.MRDP..K.SRGFGFVT.....EVDAAM.ARP
Retrocopy KELEQLQKLFIGGLSFETTDESLRNHSEQWGKLTD*VV<MRDPNTKPSRGFGFVTYTTLEEVDAAMNARP

Parental  HSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKR
          H..DGRVVEPKRAV.RE....PGAH..VKK.F.GGIKE.TEEHH.RD.FE.YGK...IEI.TDR.S..KR
Retrocopy HKVDGRVVEPKRAVSRENPQRPGAHLIVKKIFAGGIKEETEEHHFRDCFEQYGKMEVIEIMTDRGSDEKR

Parental  GFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQE-VQSSRSGRG-GNFGFGDSRGGGGNFGP
          GF.FVTFDDHD.VDKIV.QKYHT.NGHN.EVRKALS.QEM.....S.R...G.GNFG.G...G.GGN...
Retrocopy GFAFVTFDDHDFVDKIVIQKYHTVNGHNCEVRKALSKQEMAN>LHSARGQSGSGNFGGGRGGGFGGNDNF

Parental  GPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGGYDNYG
          G.G.NF...............G..G..G..G.GN.G.....GG.....G.......N.G...GG......
Retrocopy GCGGNFXXXXXXXXXXXXXXYGSSG-DGYNGFGNDGSNFRGGGSYNDFGNYNNQSSNFGPMKGGNFGGKS

Parental  GGNYGSGN-YNDFGNYNQQPSNYGPMKSGNFGGSR
          .G.YG.G...N...N......N.G...S...G..R
Retrocopy SGPYGGGG>ANTLPNHKTKVANGGSSSSSSYGSGR

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3077 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 16 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Echinops telfairi	ENSETEG00000018577	1 retrocopy	retro_etel_1368,
Macropus eugenii	ENSMEUG00000001084	2 retrocopies	retro_meug_1897, retro_meug_214,
Myotis lucifugus	ENSMLUG00000007578	1 retrocopy	retro_mluc_34,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077 , retro_ogar_3189,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
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,
Vicugna pacos	ENSVPAG00000010417	1 retrocopy	retro_vpac_616,