RetrogeneDB ID: retro_pabe_109

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:80530325..80531261(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000015596
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MED27
• Ensembl ID: ENSPPYG00000019706
• Aliases: MED27, CRSP8
• Description: Mediator of RNA polymerase II transcription subunit 27 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6U8]

Sequence

>retro_pabe_109
ATGGCGGACGTGATAAATGTCAGTGTGAACCTGGAGGCCTTTTCCCAGGCCATTAGTGCCATCCAGGCGCTGCGCTCCAG
CGTGAGCAGGGTGTTCGACTGCCTGAAGGATGGGATGCGGAACAAGGAGACGCTGGAGGGCCGGGAGAAGGCCTTCATTG
CGCACTTCCGGAACAACTTACATTCGGTCAACCGGGACCTCAAAGAGCTGGAACGTCTGAGCAATCTGGTAGGCAAGCCA
TCTGAGAACCATCCTCTTCATAACAGTGGGCTGTTAAGCCTGGATCCTGTGCAGGACAAAACTCCTCTCTATAGTCAACT
CCTTCAAGCATATAAGTGGTCAAACAAGTTGCAGTACCATGCAGGACTAGCATCTGGACTTTTAAATCAGCAGTCGTTGA
AGCGTTCTGCTAATCAGATGGGAGTATCTGCCAAACGTAGACCAAAGGCTCAGCCCACAACTCTTGTCCTACCACCTCAA
TATATTGATGATGTGATCAGCTGCATTGACAGGATGTTTCCTGAAATGTCCATCCACTTATCCAGACCCAATGGAACATC
AGCAATGCTTCTAGTGACCTTGGGAAAGGTGTTGAAAGTGATCGTCATTATGCGGAGCCTGTTCATTGATCGAACAATAG
TAAAGGGATATAACGAGAATGTCTACACAGAAGATGGCAAGCTTGATATATGGTCCAAATCCAACTATCAAGTATTCCAG
AAGGTGACAGACCACGCCACCACTGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGGATGTCGTAGTCCGATCCTTCAT
GACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCGGTGCCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCC
CGACCTGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAG

Alignment

ORF - retro_pabe_109 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFQDNLHSVNRDLNEL
          MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHF..NLHSVNRDL.EL
Retrocopy MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFRNNLHSVNRDLKEL

Parental  ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM
          ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM
Retrocopy ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM

Parental  GVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVVMRSLFID
          GVSAKRRPKAQPTTLVLPPQY.DDVIS.IDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIV.MRSLFID
Retrocopy GVSAKRRPKAQPTTLVLPPQYIDDVISCIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVIMRSLFID

Parental  RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAP
          RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQA.
Retrocopy RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAR

Parental  CQRCGKFLQDGLPPTWRDFRTLEAFHDTCRQ
          CQRCGKFLQDGLPPTWRDFRTLEAFHDTCRQ
Retrocopy CQRCGKFLQDGLPPTWRDFRTLEAFHDTCRQ

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	18.74 RPM
SRP007412_cerebellum	0.00 RPM	8.27 RPM
SRP007412_heart	0.00 RPM	6.32 RPM
SRP007412_kidney	0.00 RPM	6.30 RPM
SRP007412_liver	0.03 RPM	5.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_109 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_109 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3342
Pan troglodytes	retro_ptro_87
Gorilla gorilla	retro_ggor_130

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160563	1 retrocopy	retro_hsap_3342,
Gorilla gorilla	ENSGGOG00000010390	1 retrocopy	retro_ggor_130,
Loxodonta africana	ENSLAFG00000011556	1 retrocopy	retro_lafr_931,
Myotis lucifugus	ENSMLUG00000000364	1 retrocopy	retro_mluc_243,
Nomascus leucogenys	ENSNLEG00000012828	1 retrocopy	retro_nleu_115,
Pongo abelii	ENSPPYG00000019706	1 retrocopy	retro_pabe_109 ,
Pan troglodytes	ENSPTRG00000021492	1 retrocopy	retro_ptro_87,