RetrogeneDB ID: retro_ogar_1211

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:16175785..16176318(+)
• Located in intron of: ENSOGAG00000006619

Retrocopy information

• Ensembl ID: ENSOGAG00000027460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2R2
• Ensembl ID: ENSOGAG00000029045
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2R 2 [Source:HGNC Symbol;Acc:19907]

Sequence

>retro_ogar_1211
TACTTCAAGGAGCATCTTAAATTTCCTATTGACTACCCATATTCACCACTACCTTCAGATCCTTGACCAAACTGTGGCAC
CCCAACATTTATGGGAATGGAGATGTTTGCATTTCGATTCTTCATCCGCCTGTAGATGACTCAGGGAGTGGAGAACTGCC
CTCTGAAAGAGGGAATCCTGTTCAAAATGGGAGGACTCTTCTGTTAAATGTAATCTCACTGCTTAATGAGCCCAAGGCCT
TCTCCCCAGCCAATGTGGATGCTTCAGTTATGTTCAGAAAATGCAGAGACAGTAAAGGAAAAGACAAAGAATATGCCGAA
ATCATTGGGAAACAGGTTTCGGCCACCAAGGCCGAAGCAGAAAAGGATGGAGTGAAGATCCCCACGAGCCTGGCTGAATA
CTGCATCAAAACCGAAGTGCCTTCCAGTGACAACAGCTCAGATTTGCTTTATGACTTGTATGACATTAATGACGAAGATG
AGGAGGAGGAAGATGCTGACTGTTGTGATGATGACGATTCTGGGAATGAGGAG

Alignment

ORF - retro_ogar_1211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.64 %
• Parental protein coverage: 80.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFKAHIKFPIDYPYSP-PTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILL
          YFK.H.KFPIDYPYSP..TFR.LTK.WHPNIY.NGDVCISILHPPVDD..SGELPSER.NP.QN.RT.LL
Retrocopy YFKEHLKFPIDYPYSP<TTFRSLTKLWHPNIYGNGDVCISILHPPVDDSGSGELPSERGNPVQNGRTLLL

Parental  SVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTK
          .VISLLNEP..FSPANVDASVMFRK.RDSKGKDKEYAEII.KQVSATKAEAEKDGVK.PT.LAEYCIKT.
Retrocopy NVISLLNEPKAFSPANVDASVMFRKCRDSKGKDKEYAEIIGKQVSATKAEAEKDGVKIPTSLAEYCIKTE

Parental  VPSNDNSSDLLYDLYDDDIDDEDEEEEDADCYDDDDSGNEE
          VPS.DNSSDLLYDLY..DI.DEDEEEEDADC.DDDDSGNEE
Retrocopy VPSSDNSSDLLYDLY--DINDEDEEEEDADCCDDDDSGNEE

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_1211 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031810	1 retrocopy	retro_cfam_1138,
Dipodomys ordii	ENSDORG00000007589	1 retrocopy	retro_dord_306,
Myotis lucifugus	ENSMLUG00000006793	1 retrocopy	retro_mluc_2175,
Oryctolagus cuniculus	ENSOCUG00000023588	3 retrocopies	retro_ocun_131, retro_ocun_1719, retro_ocun_1793,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Otolemur garnettii	ENSOGAG00000029045	3 retrocopies	retro_ogar_1211 , retro_ogar_2040, retro_ogar_2946,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,