RetrogeneDB ID: retro_ptro_1520

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:41602972..41603401(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C7ORF44
• Ensembl ID: ENSPTRG00000019125
• Aliases: None
• Description: None

Sequence

>retro_ptro_1520
TGGCAAAAGTATCCAGGCAGCAGGATGCCAGTGCCTCAAGGAAAAAATGGTCCTTTTCGGCAATGTGTTCGGTACTGGGG
GTTTGGCCCTTGTGTATTACTGCATACAAAAGACTTTTTCCAGGGCTTTGTATTACCAGTTGGCATTGGAGCAGGTGCAT
AGCCATCCCAAGGCACAGGGAGCTCTGGGCCCTCTTCTCAACATTCACTGTCTCAGACTCACCAAGCACAACTTTGTGGA
CATTGCTGATGCCAAGTTGAAGATTCCTAGCTCTGGATCCAAGTCAGAGGGCCATCTCCATGTCAGCTCATCCAGAAGTG
CCCCTTTCAGAGGTGGCACCTTGATGAGGTCTTCCTAGAGCCCAAGGATGGCCAGCAGATTCCCATGTTCAAGCTCAGTG
GGGAGAATGGTGAAGAAGTGAAAAAGGAG

Alignment

ORF - retro_ptro_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.23 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WQKYAGSRRSMPLGAR-ILFHSVFYAGGFAIVYYLIQKFHSRGLYYKLAVEQLQSHPEAQEALGPPLNIH
          WQKY.GSR...P.G....LF..VF..GG.A.VYY.IQK..SR.LYY.LA.EQ..SHP.AQ.ALGP.LNIH
Retrocopy WQKYPGSRMPVPQGKN>VLFGNVFGTGGLALVYYCIQKTFSRALYYQLALEQVHSHPKAQGALGPLLNIH

Parental  YLKLIDRENFVDIADAKLKIPVSGSKSEGLLYVHSSRGG-PFQRWHLDEVFLELKDGQQIPVFKLSGENG
          .L.L....NFVDIADAKLKIP.SGSKSEG.L.V.SSR...PFQRWHLDEVFLE.KDGQQIP.FKLSGENG
Retrocopy CLRLT-KHNFVDIADAKLKIPSSGSKSEGHLHVSSSRSA<PFQRWHLDEVFLEPKDGQQIPMFKLSGENG

Parental  DEVKKE
          .EVKKE
Retrocopy EEVKKE

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	0.04 RPM	21.04 RPM
SRP007412_cerebellum	0.11 RPM	22.05 RPM
SRP007412_heart	0.00 RPM	21.98 RPM
SRP007412_kidney	0.00 RPM	29.39 RPM
SRP007412_liver	0.07 RPM	15.61 RPM
SRP007412_testis	0.00 RPM	8.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1520 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1520 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2595
Gorilla gorilla	retro_ggor_1624
Pongo abelii	retro_pabe_1914
Callithrix jacchus	retro_cjac_656

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009377	1 retrocopy	retro_amel_1871,
Canis familiaris	ENSCAFG00000031110	1 retrocopy	retro_cfam_2115,
Callithrix jacchus	ENSCJAG00000007826	1 retrocopy	retro_cjac_656,
Homo sapiens	ENSG00000106603	1 retrocopy	retro_hsap_2595,
Gorilla gorilla	ENSGGOG00000034928	1 retrocopy	retro_ggor_1624,
Macaca mulatta	ENSMMUG00000019023	1 retrocopy	retro_mmul_653,
Mustela putorius furo	ENSMPUG00000018149	1 retrocopy	retro_mputfur_1572,
Nomascus leucogenys	ENSNLEG00000003316	1 retrocopy	retro_nleu_1527,
Pongo abelii	ENSPPYG00000017606	1 retrocopy	retro_pabe_1914,
Pan troglodytes	ENSPTRG00000019125	1 retrocopy	retro_ptro_1520 ,