RetrogeneDB ID: retro_ptro_1165

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:21362281..21362583(+)
• Located in intron of: ENSPTRG00000009021

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM160
• Ensembl ID: ENSPTRG00000011200
• Aliases: None
• Description: transmembrane protein 160 [Source:HGNC Symbol;Acc:26042]

Sequence

>retro_ptro_1165
CTCCGCTTCCGGAGGTCGGTACTGCTGCCTCAGTGGCCCCGGAGCGGGGGCGCCCAGGGGTCCTTTGCCCCCAGCCACGG
CCCCCACAACGGGGCTTCGCCGCCACCTGTGTCCGAGCTGGACCGTGCAGGCGCCAGGCTCCTCTCCGAAAGGCGCACGA
GACAGCTTTCTTCTCCTGGTTCCACAATGGCCTCCTGGCATCGGGCATCGGGGTTATCACCTTCATGCAGAGTGACAGGG
ATCACGAAGCAGCATATGGCTTCTTCCGGCTGGGCGGCCTGTGTGCGGTGTGGGGCAGCGCC

Alignment

ORF - retro_ptro_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 53.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRFRRSLLPPQRPRSGGARGSFAPGHGPRAGASPPPVSELDRADAWLLR-KAHETAFL-SWFRNGLLASG
          LRFRRS.L.PQ.PRSGGA.GSFAP.HGP..GASPPPVSELDRA.A.LL..K.....FL.SWF.NGLLASG
Retrocopy LRFRRSVLLPQWPRSGGAQGSFAPSHGPHNGASPPPVSELDRAGARLLS>KGARDSFL>SWFHNGLLASG

Parental  IGVISFMQSDMGREAAYGFFLLGGLCVVWGSA
          IGVI.FMQSD...EAAYGFF.LGGLC.VWGSA
Retrocopy IGVITFMQSDRDHEAAYGFFRLGGLCAVWGSA

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	0.02 RPM	27.06 RPM
SRP007412_cerebellum	0.04 RPM	6.99 RPM
SRP007412_heart	0.00 RPM	1.08 RPM
SRP007412_kidney	0.05 RPM	12.92 RPM
SRP007412_liver	0.07 RPM	10.74 RPM
SRP007412_testis	0.00 RPM	0.21 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1165 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1165 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1828
Gorilla gorilla	retro_ggor_2165
Pongo abelii	retro_pabe_1498

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000017997	1 retrocopy	retro_etel_2100,
Homo sapiens	ENSG00000130748	1 retrocopy	retro_hsap_1828,
Gorilla gorilla	ENSGGOG00000013410	1 retrocopy	retro_ggor_2165,
Oryctolagus cuniculus	ENSOCUG00000023097	1 retrocopy	retro_ocun_1750,
Pongo abelii	ENSPPYG00000010166	1 retrocopy	retro_pabe_1498,
Pan troglodytes	ENSPTRG00000011200	1 retrocopy	retro_ptro_1165 ,
Rattus norvegicus	ENSRNOG00000015304	1 retrocopy	retro_rnor_1176,