RetrogeneDB ID: retro_ptro_2786

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:101895817..101896096(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSPTRG00000004785
• Aliases: MED21, SURB7
• Description: None

Sequence

>retro_ptro_2786
GACACCATGAACTCGCTTTCAGATCAGTTTTGCAATGCCACTGATGTGTTGCAGCAATGTGGTCTTCCTGCCTCTTTTAA
TAATATTCAGACAGCAATTAACAAAGACCAGCCAGCTAACCCTACAGAAGAATATGCTCAGCTTCTTATAGCACTGATTG
CACAAACAGCAAAAGACATTCATGTTTTGATAGATTCCTTACCCAGTGAAGAATCTACAGCTGCTTTATAGGCTACTCCC
TTATGTAAGCTAGAAGAACAAAACCATGAAGCTGCTACA

Alignment

ORF - retro_ptro_2786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 58.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAVNSLADQFCNAIGVLQQCGPPASFNNIQTAINKDQPANPTEEYAQLFAALIARTAKDIDVLIDSLPSE
          D..NSL.DQFCNA..VLQQCG.PASFNNIQTAINKDQPANPTEEYAQL..ALIA.TAKDI.VLIDSLPSE
Retrocopy DTMNSLSDQFCNATDVLQQCGLPASFNNIQTAINKDQPANPTEEYAQLLIALIAQTAKDIHVLIDSLPSE

Parental  ESTAALQAASLYKLEEENHEAAT
          ESTAAL.A..L.KLEE.NHEAAT
Retrocopy ESTAAL*ATPLCKLEEQNHEAAT

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	21.25 RPM
SRP007412_cerebellum	0.07 RPM	15.27 RPM
SRP007412_heart	0.00 RPM	14.78 RPM
SRP007412_kidney	0.00 RPM	24.16 RPM
SRP007412_liver	0.00 RPM	5.76 RPM
SRP007412_testis	0.00 RPM	101.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2786 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2786 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4105
Gorilla gorilla	retro_ggor_2756
Pongo abelii	retro_pabe_3361
Macaca mulatta	retro_mmul_2365

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Homo sapiens	ENSG00000152944	1 retrocopy	retro_hsap_4105,
Gorilla gorilla	ENSGGOG00000016313	1 retrocopy	retro_ggor_2756,
Myotis lucifugus	ENSMLUG00000007678	1 retrocopy	retro_mluc_229,
Macaca mulatta	ENSMMUG00000003218	1 retrocopy	retro_mmul_2365,
Pongo abelii	ENSPPYG00000004377	1 retrocopy	retro_pabe_3361,
Pan troglodytes	ENSPTRG00000004785	1 retrocopy	retro_ptro_2786 ,
Pteropus vampyrus	ENSPVAG00000013357	1 retrocopy	retro_pvam_449,
Ictidomys tridecemlineatus	ENSSTOG00000008391	2 retrocopies	retro_itri_1005, retro_itri_1057,