RetrogeneDB ID: retro_ptro_1614

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:76650118..76650322(-)
• Located in intron of: ENSPTRG00000012108

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_1614
GAGATGGTATATGACTGCACTAGCTCTTCCTTTGATGGAATCATTGCAATGATGAGTCCAGAGGACAGCTAGGTCTCCAA
GTGGCAGCGAGTCAGTAACTTTAAGCCAGGTACATATGCGGTGTCATTCACTGGTCACCTGCCCCAAGGAATCGTGTAGG
AGCTGAAAAGTCGAGGAGAGACCTACAAATCCAGAGACACAGCT

Alignment

ORF - retro_ptro_1614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.71 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTA
          EMVYDCTSSSFDGIIAMMSPEDS.VSKWQRVSNFKPG.YAVS.TG.LPQGIV.ELKSRG..YKSRDTA
Retrocopy EMVYDCTSSSFDGIIAMMSPEDS*VSKWQRVSNFKPGTYAVSFTGHLPQGIV*ELKSRGETYKSRDTA

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	53.93 RPM
SRP007412_cerebellum	0.07 RPM	70.62 RPM
SRP007412_heart	0.03 RPM	35.06 RPM
SRP007412_kidney	0.03 RPM	59.97 RPM
SRP007412_liver	0.03 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_1614 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1614 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2280
Gorilla gorilla	retro_ggor_1693
Pongo abelii	retro_pabe_1940
Callithrix jacchus	retro_cjac_1196

---

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,