RetrogeneDB ID: retro_ogar_2662

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873645.1:40693..41716(+)
• Located in intron of: ENSOGAG00000007646

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSOGAG00000009261
• Aliases: None
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_ogar_2662
AGGGGCCCTTGGCTCCCCAGGGCCAGGATGGCGACTGTGGAGAGCAAACTGCTGAAGAATTTCGCTTCAGAGAAGCCGGT
TACCCACAACAAGGTCTCCATTGTAGGAACTGGGTCGGTGGGTGTGGCCTGTGCTATCAGCATCTTACTAAAAGGCTTGA
GCGATGAACTCGCCCTTGTAGATATAAATGAAGAGAAACTGAAGGGTGAGACGATGGATCTTCAGCATGGCAGCTGCTTC
ATGAAAATGCCAAATATTACTTGCAGCAAAGATTACCTTATCACGGCTAATTCCAACGTAGTGATTATCACAGCAGGTGC
ACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTCCAGAGAAATGTGGCCATCTTCAAATTAATGATTTCCAGTATTA
TACAGCACAGCCCTCGCTGCAAACTGATTGTTGTTTCCAACCCAGTGGATGTCTTAACTTATGTAGCCTGGAAGTTGAGT
TCTTTTCCAGAAAACCGTGTTATAGGAAGTGGCTGTAATCTGGATACTGCTCGTTTTCGTTTTCTCATTGGGCAGAAGCT
TGGCATCCATTCTGAAAGCTGTAATGGATGGGTCCTGGGAGAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGA
ACATTGCTGGTGTCCCTTTAAAGACTCTGAACTCTGATATAGGAACTGATAAAGATCCTGAGCAATGGGAAAATATCCAC
AAAGAAGTGATTGCCAGTGCCTATGAGATTATTAAAATGAAAGGTTACACTAATTGGGGGATTGGCGTGTCTGTAGCTGA
TTTAACAGAAAGTATTTTGAAGAATCTGAAGAGAACACATCCAGTTTCTACCATAATTAAGGGCCTCTATGGAATAGATG
AAGAAGTATTCCTCAGTGTTCCTTGTGTCCTGGGAGCAAATGGTATTGCAGACCTTATAAAGATAAAGCTGACGTCTGAA
GAGGAGGCCCGTCTAAAGAAGAGTGCAACAACACTTTGGGAAATTCAGAAGGACCTTAAGCTT

Alignment

ORF - retro_ogar_2662 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 90.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGWSSPPVSKMATVKHELIKNFTSEEAIHHNKVSIIGTGSVGMACALNILLKGLSDELALVDADEGKLK
          RG.W...P...MATV...L.KNF.SE....HNKVSI.GTGSVG.ACA..ILLKGLSDELALVD..E.KLK
Retrocopy RGPWL--PRARMATVESKLLKNFASEKPVTHNKVSIVGTGSVGVACAISILLKGLSDELALVDINEEKLK

Parental  GETMDLQHGSPFMKMPNIVSSKDYLVTANSDLVIITAGVRQIKGETRLDLVERNVSVFKLMIPSIIQYSP
          GETMDLQHGS.FMKMPNI..SKDYL.TANS..VIITAG.RQ.KGETRL.LV.RNV..FKLMI.SIIQ.SP
Retrocopy GETMDLQHGSCFMKMPNITCSKDYLITANSNVVIITAGARQEKGETRLNLVQRNVAIFKLMISSIIQHSP

Parental  WCKMIIVTNPVDILTYVAWKLSAFPKNRVIGSGCNLDTARFRYFIGQRLGIHSESCHGLVLGEHGDSSVP
          .CK.I.V.NPVD.LTYVAWKLS.FP.NRVIGSGCNLDTARFR..IGQ.LGIHSESC.G.VLGEHGDSSVP
Retrocopy RCKLIVVSNPVDVLTYVAWKLSSFPENRVIGSGCNLDTARFRFLIGQKLGIHSESCNGWVLGEHGDSSVP

Parental  IWSGVNIAGVPLKDLNPDIGTDKDPEQWENVHKKVVSSGYEMLKMKGYTSWGVSLSVADLTESILKNLRR
          .WSGVNIAGVPLK.LN.DIGTDKDPEQWEN.HK.V..S.YE..KMKGYT.WG...SVADLTESILKNL.R
Retrocopy VWSGVNIAGVPLKTLNSDIGTDKDPEQWENIHKEVIASAYEIIKMKGYTNWGIGVSVADLTESILKNLKR

Parental  VHPVSTLSKGLYGINEEIFLSVPCILGENGITDLIKLKLTPEEEARLQKSADTLWEIQKRLKL
          .HPVST..KGLYGI.EE.FLSVPC.LG.NGI.DLIK.KLT.EEEARL.KSA.TLWEIQK.LKL
Retrocopy THPVSTIIKGLYGIDEEVFLSVPCVLGANGIADLIKIKLTSEEEARLKKSATTLWEIQKDLKL

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_2662 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 9 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662 ,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,