RetrogeneDB ID: retro_ptro_735

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:8734696..8734978(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSPTRG00000009451
• Aliases: None
• Description: None

Sequence

>retro_ptro_735
ACTATAGACCAGTTTGAATATGATGGTTGTGACTATTGAGATGCATGTCTACAGATGAAGGGTAACTGAGAGATGCTCTA
TGGCTGCACCAGCTCCTCCTTTGATGGAATCATTGCGATGATGAGTCCAGAGGACAGCTGGGTCTCCAACTGGCAGCGAG
TCAATAACTTTAAGCCAGGTGTATATGCGGTGTCAACCACTGGTCGCTTGCCCTAAGGAACCGTGCGGGAGCTGAAAAGT
TGAGGAGTGGCCTACAAATCCAAAGACACAGCTATAAAGACC

Alignment

ORF - retro_ptro_735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRL
          TIDQFEYDGCD..DA.LQMKGN.EM.Y.CTSSSFDGIIAMMSPEDSWVS.WQRV.NFKPGVYAVS.TGRL
Retrocopy TIDQFEYDGCDY*DACLQMKGN*EMLYGCTSSSFDGIIAMMSPEDSWVSNWQRVNNFKPGVYAVSTTGRL

Parental  PQGIVRELKSRGVAYKSRDTAIKT
          P.G.VRELKS.GVAYKS.DTAIKT
Retrocopy P*GTVRELKS*GVAYKSKDTAIKT

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	53.93 RPM
SRP007412_cerebellum	0.04 RPM	70.62 RPM
SRP007412_heart	0.03 RPM	35.06 RPM
SRP007412_kidney	0.03 RPM	59.97 RPM
SRP007412_liver	0.00 RPM	46.48 RPM
SRP007412_testis	0.00 RPM	66.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_735 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_735 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1081
Gorilla gorilla	retro_ggor_854

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017524	2 retrocopies	retro_cfam_1399, retro_cfam_553,
Homo sapiens	ENSG00000213246	2 retrocopies	retro_hsap_1081, retro_hsap_2280,
Gorilla gorilla	ENSGGOG00000007232	2 retrocopies	retro_ggor_1693, retro_ggor_854,
Macropus eugenii	ENSMEUG00000010164	1 retrocopy	retro_meug_2079,
Myotis lucifugus	ENSMLUG00000025583	1 retrocopy	retro_mluc_761,
Macaca mulatta	ENSMMUG00000007579	2 retrocopies	retro_mmul_1005, retro_mmul_842,
Mus musculus	ENSMUSG00000020485	2 retrocopies	retro_mmus_2857, retro_mmus_633,
Nomascus leucogenys	ENSNLEG00000008159	3 retrocopies	retro_nleu_1619, retro_nleu_1962, retro_nleu_2714,
Oryctolagus cuniculus	ENSOCUG00000025823	2 retrocopies	retro_ocun_1613, retro_ocun_1636,
Pongo abelii	ENSPPYG00000008233	1 retrocopy	retro_pabe_1940,
Pan troglodytes	ENSPTRG00000009451	2 retrocopies	retro_ptro_1614, retro_ptro_735 ,
Pteropus vampyrus	ENSPVAG00000002320	1 retrocopy	retro_pvam_477,
Rattus norvegicus	ENSRNOG00000007845	3 retrocopies	retro_rnor_1255, retro_rnor_1973, retro_rnor_556,