RetrogeneDB ID: retro_ptro_22

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:37253848..37254256(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000028614
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM183A
• Ensembl ID: ENSPTRG00000000624
• Aliases: None
• Description: family with sequence similarity 183, member A [Source:HGNC Symbol;Acc:34347]

Sequence

>retro_ptro_22
ATGGCGGGACACCCGAAAGAGAGGGTGGTCACAGATGAGGTCCATCAGAACCAGATCTTGCGGGAGCTGTACCTCAAAGA
GTTACGAACCCAGAAACTCTACACGCAGTACCACGTGAATCCCCTGCGCAAGGTTCACAGGATTACGAGGAAGCCTATGT
CTTGGCATGATAACCTGGAGGAACCCGCAGACGCCAGGTTTCTGAATCTCATTCACCATGCTGCCCAGGGGCCAACGAAG
AAGTACCCAGAGGCACAGACTGAAAACCAGGAAATTGGGTGGGACTCAGAAGCCTTGGTCGACCCAGAACGCCGTGACCA
CAGGATGAACCACTTCAGGGTCTACAATGACATCACTCTGTACAAAGCTAAAATGTGGAGCTTGGGAGAAGATGATCGCC
ACAAGTAG

Alignment

ORF - retro_ptro_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGHPKEKVIPDEVHQNQILRELYLKELRTQKLYTQYHVNPLRKIHTVTRKPMSWHDNLEEPADARFLNL
          MAGHPKE.V..DEVHQNQILRELYLKELRTQKLYTQYHVNPLRK.H..TRKPMSWHDNLEEPADARFLNL
Retrocopy MAGHPKERVVTDEVHQNQILRELYLKELRTQKLYTQYHVNPLRKVHRITRKPMSWHDNLEEPADARFLNL

Parental  IHHAAQGPRKKYPETQTENQEVGWDLEPLINPERHDRRLNHFRVCSDITLYKAKTWGLG-DDHHK
          IHHAAQGP.KKYPE.QTENQE.GWD.E.L..PER.D.R.NHFRV..DITLYKAK.W.LG.DD.HK
Retrocopy IHHAAQGPTKKYPEAQTENQEIGWDSEALVDPERRDHRMNHFRVYNDITLYKAKMWSLGEDDRHK

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	0.21 RPM	0.02 RPM
SRP007412_cerebellum	0.25 RPM	0.07 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.63 RPM	0.13 RPM
SRP007412_liver	0.43 RPM	0.00 RPM
SRP007412_testis	14.65 RPM	10.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_22 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_22 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1
Gorilla gorilla	retro_ggor_69
Pongo abelii	retro_pabe_48

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005339	1 retrocopy	retro_cfam_671,
Callithrix jacchus	ENSCJAG00000003315	1 retrocopy	retro_cjac_323,
Homo sapiens	ENSG00000186973	1 retrocopy	retro_hsap_1,
Gorilla gorilla	ENSGGOG00000010892	2 retrocopies	retro_ggor_1704, retro_ggor_69,
Nomascus leucogenys	ENSNLEG00000013230	3 retrocopies	retro_nleu_147, retro_nleu_2537, retro_nleu_2865,
Pongo abelii	ENSPPYG00000001457	1 retrocopy	retro_pabe_48,
Pan troglodytes	ENSPTRG00000000624	1 retrocopy	retro_ptro_22 ,