RetrogeneDB ID: retro_ogar_797

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873527.1:39666687..39667368(-)
• Located in intron of: ENSOGAG00000032172

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSOGAG00000008710
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_ogar_797
GGAGCCTGAGGAGGTGCTGCTGGAGCCCGAGCCCAAAGAGGAGCCACCCCCATCCCTCAGCAGCCAGGAGGAGGAAGAGC
CAGGACTGGTCGAGGGTGACCTGGGGATGGCGCCATTGAGGACCTGGAGCTGGAAGCGATCATAGTTCGGTTCAGGGAGA
TGGAGGAAGAAGCTGAGAAGTTAAAAGAGCTACATAACGAGGTAGAGGAAGCGGATCACCACCAGGCAATGCTGGCCCAG
TGATCATGTCCATTTAAGAGAAGATGAAGGCTGATGCCCATTCCATCTATGTTGGCAATGTGGACTGTGGTGCAACAGCA
GAAGAGCTAGAAGCTCACTTTCATGGCTGTGGTTCAGTCAACCGTGTTACCATACCCTGTGACAAATTTAGTGGCCATCC
CAAAGGGTTTGCCTATATAGAGTTCTTAGACAGAGTCAGTGAGGACTTCCCTGGCCTTAGATGAGTCCCTATTTAGAGGA
AGACAAATCAAGGTGATCCCAAAATGAACCAACAGACCAGGCATCAGCACAACAGACCAGGGTTTCCCAGGAGCCTGCTA
CCGTGCCAGGACCACCAACTATAACAGTTCCCACTCTCAACTGCACAGTGCTTTTAACAGCAGGCCCCAGGGTGGCATTT
ACAGGGGCCTGGCTAGAGAGACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_ogar_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 73.53 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAPGPGPGSGAP-GSQEEEEEPGLVEGDPGDGAIEDPELE--AIKARVREMEEEAEKLK-ELQNEVEKQM
          GA.G...G..A..G.......PG......G.G...D...E.....A......E..E....E.........
Retrocopy GA*GGAAGARAQRGATPIPQQPGGGRARTGRG*PGDGAIEDLELEAIIVRFREMEEEAE<EVKRAT*RGR

Parental  NMSPPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGH-PKGFA
          ....PPGNAGPVIMSI.EKM.ADA.SIYVGNVD.GATAEELEAHFHGCGSVNRVTI.CDKFSGH.PKG..
Retrocopy GSGSPPGNAGPVIMSI*EKMKADAHSIYVGNVDCGATAEELEAHFHGCGSVNRVTIPCDKFSGH>PKGLP

Parental  YIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNS
          .I..S..ESVRTSLALDESLFRGRQIKVIPK.TNRPGISTTD.GFP.A.YRARTTNYNSS.S...S.FNS
Retrocopy -I*SS*TESVRTSLALDESLFRGRQIKVIPK*TNRPGISTTDQGFPGACYRARTTNYNSSHSQLHSAFNS

Parental  RPRGRVYRGRARATSWYSPY
          RP.G..YRG.AR.TSWYSPY
Retrocopy RPQGGIYRGLARETSWYSPY

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_797 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797 ,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,