RetrogeneDB ID: retro_pabe_1940

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:34982290..34982494(+)
• Located in intron of: ENSPPYG00000012255

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT4H1
• Ensembl ID: ENSPPYG00000008233
• Aliases: None
• Description: transcription elongation factor SPT4 [Source:RefSeq peptide;Acc:NP_001129015]

Sequence

>retro_pabe_1940
GAGATGGTATATGACTGCACTAGCTCTTCCTTTGACGGAATCATTGCAATGATGAGTCCAGAGGACAGTTAGGTCTCCAA
GTGGCAGCGAGTCACTAACTTTAAGCCAGGTACATATGCGGTGTCATTCACTGGTCACCTGCCCCAAGGAATCGTGTAGG
AGCTGAAAAGTCGAGGAGCGACCTACAAATCCAGAGACACAGCT

Alignment

ORF - retro_pabe_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTA
          EMVYDCTSSSFDGIIAMMSPEDS.VSKWQRV.NFKPG.YAVS.TG.LPQGIV.ELKSRG..YKSRDTA
Retrocopy EMVYDCTSSSFDGIIAMMSPEDS*VSKWQRVTNFKPGTYAVSFTGHLPQGIV*ELKSRGATYKSRDTA

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	50.43 RPM
SRP007412_cerebellum	0.00 RPM	51.32 RPM
SRP007412_heart	0.00 RPM	26.25 RPM
SRP007412_kidney	0.13 RPM	49.69 RPM
SRP007412_liver	0.03 RPM	40.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1940 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1940 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2280
Pan troglodytes	retro_ptro_1614
Gorilla gorilla	retro_ggor_1693
Callithrix jacchus	retro_cjac_1196

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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,