RetrogeneDB ID: retro_ptro_1246

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:2115172..2115589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM207A
• Ensembl ID: ENSPTRG00000013995
• Aliases: None
• Description: family with sequence similarity 207, member A [Source:HGNC Symbol;Acc:15811]

Sequence

>retro_ptro_1246
TCCATCAGGAGAGGTGCAGAGGCCAAGACCGTTTTGCCCAAGGAGAAAATGAAGCTGAGGCGTGAGCAATGGTTGCAGAA
AATCGAAGCCATAAAACTGGCTGAGCAGAAGCACAGGGAGGAGCGGAGGTAGAGGGCCAGGGTGGTGGTGGGGGACCTGC
ACCTGCTCAGGGGTGCCCTACCTGAGCTGCTGGGGCTTGAGGCTGGCAGCCGGGGCCAAGCCTGCAGCAGGGAGAGCAAC
AAGCCCTGGCCCTCAGAGCTCAGCCGGATGAGCGCAGCCCAGAGACAGCAGCTTCTCGAGGAAGAAAGGACTCGTTTTCA
GGAGCTGCTGGCCAGTCCGGCCTACAGAGCCAGCCCCCTGTTAGCCATCGGGCAGACGCTGGCCCGGCAGATGCAGCTGG
AAGATGGCGGCCAGCTC

Alignment

ORF - retro_ptro_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.43 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLSSGAEAKTVLPKKEKMKLRREQWLQKIEAIKLAEQKHREERRRRATVVVGDLHPLRDALPELLGLEAG
          S...GAEAKTVLPK.EKMKLRREQWLQKIEAIKLAEQKHREERR.RA.VVVGDLH.LR.ALPELLGLEAG
Retrocopy SIRRGAEAKTVLPK-EKMKLRREQWLQKIEAIKLAEQKHREERR*RARVVVGDLHLLRGALPELLGLEAG

Parental  SRRQARSRESNKPRPSELSRMSAAQRQQLLEEERTRFQELLASPAYRASPLVAIGQTLARQMQLEDGGQL
          SR.QA.SRESNKP.PSELSRMSAAQRQQLLEEERTRFQELLASPAYRASPL.AIGQTLARQMQLEDGGQL
Retrocopy SRGQACSRESNKPWPSELSRMSAAQRQQLLEEERTRFQELLASPAYRASPLLAIGQTLARQMQLEDGGQL

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	0.00 RPM	6.92 RPM
SRP007412_cerebellum	0.00 RPM	5.16 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	6.17 RPM
SRP007412_liver	0.00 RPM	7.17 RPM
SRP007412_testis	0.00 RPM	6.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1246 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1246 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1167

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160256	4 retrocopies	retro_hsap_1167, retro_hsap_1916, retro_hsap_2494, retro_hsap_4325,
Gorilla gorilla	ENSGGOG00000014482	1 retrocopy	retro_ggor_1554,
Loxodonta africana	ENSLAFG00000010542	1 retrocopy	retro_lafr_919,
Pan troglodytes	ENSPTRG00000013995	3 retrocopies	retro_ptro_1246 , retro_ptro_1446, retro_ptro_803,