RetrogeneDB ID: retro_ptro_43

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:23240016..23240250(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039103
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000033768
• Aliases: None
• Description: None

Sequence

>retro_ptro_43
ATGCCCAAGTGCCCCGCGTGCGACAAGGTGTACCTCGCCGAGAGGGTGACCTCTCTAGGCAAGGACTGGCATCGGCCCTG
CCTGAAGTGTGAGAAATGTGGGAAGACACTGACTTCCGGGGGCCACGCTGAGCATGAAGGCAAACCCTACGGCAACCACA
CCTGCTATGCCGCCATGTTTGGGCCTACTAAAGGCTTTGGGCGGGGTGGACCCGAGAGCCACACTTTCAAGTAA

Alignment

ORF - retro_ptro_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYAAMFGP-KGFGRGGAESHTFK
          ERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPY.NH.CYAAMFGP.KGFGRGG.ESHTFK
Retrocopy ERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYGNHTCYAAMFGPTKGFGRGGPESHTFK

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	0.02 RPM	3.88 RPM
SRP007412_cerebellum	0.04 RPM	2.08 RPM
SRP007412_heart	0.61 RPM	29.50 RPM
SRP007412_kidney	0.24 RPM	9.99 RPM
SRP007412_liver	0.10 RPM	6.51 RPM
SRP007412_testis	0.00 RPM	0.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_43 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_43 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_43 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2550
Gorilla gorilla	retro_ggor_3

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114,
Pan troglodytes	ENSPTRG00000001836	2 retrocopies	retro_ptro_1920, retro_ptro_1922,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43 ,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,