RetrogeneDB ID: retro_ogar_2865

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873673.1:3408267..3408726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSOGAG00000003865
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_ogar_2865
ATGGCTCATTCCTAGTGCCTCTCAGTGCTTGCCTGCTGAGCTGTCTACACCAACTTCTCATGCACCCAAAAAGGAATTTT
CCTGTTTGCTGAGATTATTATATTGGGCCTGGCAATTCTAATCTGCTTTAGTGCCTTGACACCAGGTACTCCTCCCTGTG
GGTGGTTGAAATGATCCTTGCTGCTATCTTCTTTGCCATCCACTCAATGTGAATTAAGCGTGAAGATACCATTCATCAAT
TGGCCCTGAAGTGATTTCTTCTGGACCCTCACTGAGGCAACCCTCTACCTGATCATCTCCACTGTTGTCCTTATTGACAG
AGGAAATTGCTCTAAAATCATTGCAGGGGTTCTGGGCCTAATCGCTCCATGCCTTTTTGGGTATGGTGCCTACTTCACCT
TCTCACTTCAGCAGCAGAGACATATAGCAGCCGCCATTGATCCTTCAGATGGCCCAGTA

Alignment

ORF - retro_ogar_2865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPGCWAACTNFSRTRKGVLLLAEIILC-LVILICFSASTPG-YSSLSVIEMIFAAIFFVIY-
          MA.S..LS...C.A..TNFS.T.KG..L.AEII...L.ILICFSA.TPG.YSSL.V.EMI.AAIFF.I..
Retrocopy MAHS*CLSVLAC*AVYTNFSCTQKGIFLFAEIIILGLAILICFSALTPG<YSSLWVVEMILAAIFFAIH>

Parental  MCDLNTKIPLINWPWSDFFRTLIGAILYLITSIVVLIERGNPSKIVAGVLGLIATCLFGYDAYVTFPLRQ
          .C.L..KIP.INWP.SDFF.TL..A.LYLI.S.VVLI.RGN.SKI.AGVLGLIA.CLFGY.AY.TF.L.Q
Retrocopy QCELSVKIPFINWP*SDFFWTLTEATLYLIISTVVLIDRGNCSKIIAGVLGLIAPCLFGYGAYFTFSLQQ

Parental  QKHTAAPTEPADGPV
          Q.H.AA...P.DGPV
Retrocopy QRHIAAAIDPSDGPV

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_2865 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 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865 , retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,