RetrogeneDB ID: retro_ogar_2342

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873613.1:5639485..5640132(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000033255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSOGAG00000030474
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_ogar_2342
AGCCCCGAGCACGCCGGCTGGACCGAAGCGCTGCGGGCCGCCGTGGCCGAGCTGCGCGCCGGCGCCGTGTAGGCTGTCCC
CGCCGATACGCTGCACGGCCTGGCCTGCTCAGCGAGTCGCTCGGCGGCGCTGTGCGATGTGTACCGCTTCAAAGGCTGCA
GCAAGGCCAACCCCCTGGCCGTATGCCTGGGCGGGTGGCCGATGTCTACGGGTACTGCCATGTGAGATTACCAGATGAGC
TCCTGAACGACTTGTTGCCAGGCCCAGTGACTCTGGGGATGGAACGCACAGGCACACTCAACAAGGGCCTGATCCGCTTT
ACTCCTCTCGTAGGCATCTGGATTTCTGACCACGCCTTTATGCAAGATTTGGCCACGATGTTTGGGGAACCTCTTGCACT
CAGTAGTGCCAACCTCAGCTTCCAGGCCAGTTCTCTGAATGTTGAGGAGTTCCAACACCTCTGGCCTCGTTTGTCTTTGG
TCATTAATGGAGGACCAATTGGGGATAGCCAGAGCTCAGAGTGTTGCCTGGACTGAACTGTTATTGATTTATCTATACCT
AGAAAGCTTGGCATTATTTGTCCTGGCTGTGCCCTAGAAAGAACTACAGCTGTCCTCCAACAGAAGTACAGGCTGCTCCC
CTCACAT

Alignment

ORF - retro_ogar_2342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.11 %
• Parental protein coverage: 78.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSERAGWTEALRAAVAELRAGAVLAVPTDTLYGLACSASCSAALRDVYRLKGRSEAKPLAVCLG-RVADV
          S.E.AGWTEALRAAVAELRAGAV.AVP.DTL.GLACSAS.SAAL.DVYR.KG.S.A.PLAVCLG.RVADV
Retrocopy SPEHAGWTEALRAAVAELRAGAV*AVPADTLHGLACSASRSAALCDVYRFKGCSKANPLAVCLG<RVADV

Parental  YRYCHVRVPEELLKDLLPGPVTLVMERTEALNKDLNPFTPLVGIRIPDHTFMQDLSQMFGEPLALTSANL
          Y.YCHVR.P.ELL.DLLPGPVTL.MERT..LNK.L..FTPLVGI.I.DH.FMQDL..MFGEPLAL.SANL
Retrocopy YGYCHVRLPDELLNDLLPGPVTLGMERTGTLNKGLIRFTPLVGIWISDHAFMQDLATMFGEPLALSSANL

Parental  SSQASSLNVEEFQHLWPHLSLVIDGGPIGDSQSPECRLGSTVVDLSVPGKFGIIRPGCALERTTAILQQK
          S.QASSLNVEEFQHLWP.LSLVI.GGPIGDSQS.EC.L..TV.DLS.P.K.GII.PGCALERTTA.LQQK
Retrocopy SFQASSLNVEEFQHLWPRLSLVINGGPIGDSQSSECCLD*TVIDLSIPRKLGIICPGCALERTTAVLQQK

Parental  YRLLPSH
          YRLLPSH
Retrocopy YRLLPSH

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_2342 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342 ,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,