RetrogeneDB ID: retro_ptro_2203

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:156258055..156258918(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OBFC1
• Ensembl ID: ENSPTRG00000002919
• Aliases: None
• Description: None

Sequence

>retro_ptro_2203
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTCATCCACTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCGTTGAGCAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACACGTGCAGAGAAGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGAGCTGCCCATTAATCTACAGGGAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
AAAGAATTCCCCATAAAGAACAGAGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGGATCCTTTGCTGTCCCTTGC
TAACCAGCCTGTTACTGACAGTGCCTGCTCTGAACAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATTCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGTATAGGAAAATCCACTGGATAATTCAGAAAGACTACCAGAAACCAAATCACCCGAA
GAAGGGCTGCCACTTCCTGCACATCTTGGCCTGCGCTCACCCTGAGCATCTGCCCAGTTCTAGTTAGGGCTATGTTGCAG
CAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC

Alignment

ORF - retro_ptro_2203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.01 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA
          TGVINCIC.K.L.N....S.AP.AARELS.TS.LKKLQ.T.EQRTKIE.GD....RG...T.REE.EI.A
Retrocopy TGVINCIC*KILSNIKFSSTAPNAARELSFTSILKKLQDTVEQRTKIETGDMF*IRGYVYTCREE*EIYA

Parental  TAYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFHSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
          TAYYKVDDPVWNIQIAR..ELP..IYR.V...PFH...LEKEEALSNPG.L...SL..LLSEKAKEF...
Retrocopy TAYYKVDDPVWNIQIARVFELPI>IYREV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAKEFPIK

Parental  NRVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLQEKGLVFQKDDGFD
          NRVQ.F.QQELEMV..LLSLANQPV..SACS.Q.NFKKD.T.KAI.SIF.NAIQ.LQEKGLVFQKD.GFD
Retrocopy NRVQTFDQQELEMVDPLLSLANQPVTDSACSEQGNFKKDITFKAIYSIF*NAIQQLQEKGLVFQKDGGFD

Parental  NLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
          NL..VTR.DKDL.RKIH.IIQ.D.QKPNH..KGCHFLHILACA..LSI.P.L..A.LQQVLELLEDQSD.
Retrocopy NLCCVTRKDKDLYRKIHWIIQKDYQKPNHPKKGCHFLHILACAH>LSICPVLVRAMLQQVLELLEDQSDL

Parental  VSTMEHYYT
          .STMEH.Y.
Retrocopy ISTMEHHYS

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	5.56 RPM
SRP007412_cerebellum	0.04 RPM	6.13 RPM
SRP007412_heart	0.09 RPM	13.03 RPM
SRP007412_kidney	0.00 RPM	16.89 RPM
SRP007412_liver	0.00 RPM	7.23 RPM
SRP007412_testis	0.00 RPM	35.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2203 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2203 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3257
Gorilla gorilla	retro_ggor_2219
Pongo abelii	retro_pabe_2701
Macaca mulatta	retro_mmul_2050
Callithrix jacchus	retro_cjac_1791

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203 ,