RetrogeneDB ID: retro_pabe_3361

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:110213045..110213348(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED21
• Ensembl ID: ENSPPYG00000004377
• Aliases: None
• Description: mediator of RNA polymerase II transcription subunit 21 [Source:RefSeq peptide;Acc:NP_001124922]

Sequence

>retro_pabe_3361
AGTGATCAGCTCATGCAGCTGTAAAACACCATGAACTTGCTTGCAGATCAGTTTTGCAATGCCACTGATGTGTTGCAGCA
ATGTGGTCTTCCTGCCTCTTTTAATAATATTCAGACAGCAATTAACAAAGACCAGCCAGCTAACCCTACAGAAGAATATG
CTCAGCTTCTTATAGCACTGATTGCACAAACAGCAAAAGACATTCATGTTTTGATAGATTCCTTACCCAGTGAAGAATCT
ACAGCTGCTTCATAGGCTACTCCCTTATGTAAGCTAGAAGAACAAAACCATGAAGCTGCTACA

Alignment

ORF - retro_pabe_3361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 70.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADRLTQLQDAVNSLADQFCNAIGVLQQCGPPASFSNIQTAINKDQPANSTEEYAQLFAALIARTAKDIDA
          .D.L.QL....N.LADQFCNA..VLQQCG.PASF.NIQTAINKDQPAN.TEEYAQL..ALIA.TAKDI..
Retrocopy SDQLMQL*NTMNLLADQFCNATDVLQQCGLPASFNNIQTAINKDQPANPTEEYAQLLIALIAQTAKDIHV

Parental  RNCIPLEEESFSALFAASLYKLEEENHEAAT
          .......EES..A..A..L.KLEE.NHEAAT
Retrocopy LIDSLPSEESTAAS*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	0.22 RPM	4.48 RPM
SRP007412_cerebellum	0.24 RPM	6.69 RPM
SRP007412_heart	0.36 RPM	7.04 RPM
SRP007412_kidney	0.33 RPM	5.57 RPM
SRP007412_liver	0.28 RPM	4.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3361 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3361 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4105
Pan troglodytes	retro_ptro_2786
Gorilla gorilla	retro_ggor_2756
Macaca mulatta	retro_mmul_2365

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011670	1 retrocopy	retro_amel_108,
Dasypus novemcinctus	ENSDNOG00000010041	1 retrocopy	retro_dnov_998,
Echinops telfairi	ENSETEG00000006223	1 retrocopy	retro_etel_1141,
Felis catus	ENSFCAG00000030691	1 retrocopy	retro_fcat_1101,
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,
Nomascus leucogenys	ENSNLEG00000005431	1 retrocopy	retro_nleu_573,
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,