RetrogeneDB ID: retro_ptro_2316

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:181717446..181717726(-)
• Located in intron of: ENSPTRG00000017636

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSPTRG00000021885
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_ptro_2316
TATTTTGTCAGCTACGTGTGTGATCTGCACACCAAAATACCATTCATCAATTGGCCCTGGAGTCATTTCTTCCAAACTCT
CTTAGCAGTGATCCTCTAGCTAATCACCTCCATTATCGACAATGTTGAGAAAGGAAACCACTCCAAAATCATCGCAGGGG
TACTGGGCCTAATTGCTAAGGGCCTCTTTGGCTTTAATGCCTACGTCAACCTTCCCCTTTCAGTAGCAAAGATATACAAG
ATATACAGCAGCCCCCACTGGCCCCACAGATGGCCCAGTG

Alignment

ORF - retro_ptro_2316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.15 %
• Parental protein coverage: 59.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFVVYMCDLHTKIPFINWPWSDFLRTLIAAILYLITSIVVLVERGNHSKIVAGVLGLIATCLFGYDAYV-
          .FV.Y.CDLHTKIPFINWPWS.F..TL.A.IL.LITSI...VE.GNHSKI.AGVLGLIA..LFG..AYV.
Retrocopy YFVSYVCDLHTKIPFINWPWSHFFQTLLAVIL*LITSIIDNVEKGNHSKIIAGVLGLIAKGLFGFNAYV>

Parental  TFPVRQPRHT---AAPTDPADGPV
          TFP....R.T...AAPT.P.DGPV
Retrocopy TFPFQ*QRYTRYTAAPTGPTDGPV

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
SRP007412_brain_prefrontal_cortex	0.04 RPM	1.98 RPM
SRP007412_cerebellum	0.00 RPM	10.97 RPM
SRP007412_heart	0.00 RPM	10.58 RPM
SRP007412_kidney	0.03 RPM	9.62 RPM
SRP007412_liver	0.00 RPM	12.05 RPM
SRP007412_testis	0.00 RPM	3.90 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2316 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2316 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3411
Macaca mulatta	retro_mmul_2124

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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,