RetrogeneDB ID: retro_ecab_971

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:40518086..40518541(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006661
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSECAG00000000216
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_ecab_971
ATGGCGGATTCCGAGCTTCGCTCGGCCCCCGGCTGCTGCGTCCACTGCACCAACTTCTTGCGCAGCCGAAAGGGAATTCT
CCTGTTTGCTGAGATTATATTTTGCCTGATGATTGTGATCTGCTTCAGTGTCTCAGCACCAAAATACTCCAGCCTGTCGG
TGGTGGAGCTGATCCTTGCTGTTTTCTTTTTTGTCATCTACATGTGTGACCTGCACCCCAAGATACGATTCATCAACTGG
CCTTGGAGTGATTTCTTCCGAACCTTCATAGCAGCGATCCTCTATCTGACCACCTCCATTATTGTCCTTGTTCAGAGAGG
ACACCGCTCCAAAATCACCGCAGGGGCACTGGGCTTAGTTGCCACGTGCCTCTTTGGCTATGATGCCTATGTCACCTTAC
CCTGGGAGAAATAAAGACATATAGTAGCCTCTACTGAACCGCAGATGGCCCGGTG

Alignment

ORF - retro_ecab_971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPGCWTACTNFWRTRKGILLFAEIVLCLVILICFSASTSAYSSLSVIEMILAAIFFVIYMCD
          MADSE..SAPGC...CTNF.R.RKGILLFAEI..CL.I.ICFS.S...YSSLSV.E.ILA..FFVIYMCD
Retrocopy MADSELRSAPGCCVHCTNFLRSRKGILLFAEIIFCLMIVICFSVSAPKYSSLSVVELILAVFFFVIYMCD

Parental  LHNKIQIINWPWSDFFRTLIAAILYLITSIVVLVNERNHSRITAGVLGLIATCLFGYDAYTTFPLRQQRH
          LH.KI..INWPWSDFFRT.IAAILYL.TSI.VLV.....S.ITAG.LGL.ATCLFGYDAY.T.P....RH
Retrocopy LHPKIRFINWPWSDFFRTFIAAILYLTTSIIVLVQRGHRSKITAGALGLVATCLFGYDAYVTLPWEK*RH

Parental  SAAPTDP-ADGPV
          ..A.T.P.ADGPV
Retrocopy IVASTEP<ADGPV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	54.84 RPM
SRP021940_cerebellum	0.10 RPM	4.83 RPM
SRP021940_embryo	0.20 RPM	4.35 RPM
SRP021940_placental_villous	0.00 RPM	92.61 RPM
SRP021940_synovial_membrane	0.00 RPM	56.63 RPM
SRP021940_testis	60.49 RPM	5.05 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_971 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_971 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_971 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_73

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Equus caballus	ENSECAG00000000216	1 retrocopy	retro_ecab_971 ,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Pteropus vampyrus	ENSPVAG00000011770	2 retrocopies	retro_pvam_1214, retro_pvam_810,