RetrogeneDB ID: retro_pabe_1498

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30365181..30365584(-)
• Located in intron of: ENSPPYG00000008188

Retrocopy information

• Ensembl ID: ENSPPYG00000008189
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM160
• Ensembl ID: ENSPPYG00000010166
• Aliases: None
• Description: transmembrane protein 160 [Source:HGNC Symbol;Acc:26042]

Sequence

>retro_pabe_1498
CTCCGCTTCCGGAGGTCGCTACTGCCGCCTCAGTGGCCCCGCAGCGGGGGCGCCCAGGGGTCCTTCGCCCCCGGCCACGG
CCCCCGCAACGAGGCTTCGCCGCCACCTGTGTCCGAGCTGGACCGTGCAGGCGCCAGGCTCCTCCGAAAGGCGCACGAGA
CAGCTTTCTTCTCCTGCTTCCACAATGGCCTCCTGGCATCGGGCATCGGGGGTTATCTCCTTCATGCAGAGTGACATGGA
TCGCGAAGCAGCATATGGCTTCTTCCTGCTGGGAGGCCTGTGTGCGGTGTGGGGCAGCGCCTCGTACGTGGTGGGCCTGG
CAGCGCTGCGGGGGCCCATGCAGCTGACGCTAGGGGGCGCAGCTGCGGGCGCTGTACTCGCCGCCAGCCCGCTCTGGGTG
TGC

Alignment

ORF - retro_pabe_1498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.4 %
• Parental protein coverage: 79.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRFRRSLLPPQRPRSGGARGSFAPGHGPRAGASPPPVSELDRADAWLLRKAHETAFLSWFRNGLLASGI-
          LRFRRSLLPPQ.PRSGGA.GSFAPGHGPR..ASPPPVSELDRA.A.LLRKAHETAF.S.F.NGLLASGI.
Retrocopy LRFRRSLLPPQWPRSGGAQGSFAPGHGPRNEASPPPVSELDRAGARLLRKAHETAFFSCFHNGLLASGI>

Parental  GVISFMQSDMGREAAYGFFLLGGLCVVWGSASYAVSLAALRGPMQLTLGSAAVGVGAVLAASLLWAC
          GVISFMQSDM.REAAYGFFLLGGLC.VWGSASY.V.LAALRGPMQLTLG.AA...GAVLAAS.LW.C
Retrocopy GVISFMQSDMDREAAYGFFLLGGLCAVWGSASYVVGLAALRGPMQLTLGGAA--AGAVLAASPLWVC

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	0.28 RPM	1.44 RPM
SRP007412_cerebellum	0.00 RPM	0.36 RPM
SRP007412_heart	0.03 RPM	0.30 RPM
SRP007412_kidney	0.23 RPM	1.19 RPM
SRP007412_liver	0.21 RPM	1.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1498 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1498 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1828
Pan troglodytes	retro_ptro_1165
Gorilla gorilla	retro_ggor_2165

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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,