RetrogeneDB ID: retro_ptro_87

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:35137064..35138000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040617
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MED27
• Ensembl ID: ENSPTRG00000021492
• Aliases: None
• Description: mediator complex subunit 27 [Source:HGNC Symbol;Acc:2377]

Sequence

>retro_ptro_87
ATGGCGGACGTGATAAATGTCACTGTGAACCTGGAGGCCTTTTCCCAGGCCATTAGTGCCATCCAGGCCCTGCACTCCAG
CGGGAGCAGGGTGTTCGACTGCCTGAAGGATGGGATGCGGAACAAGGAGACGCTGGAGGGCCGGGAGAAGGCCTTCATTG
CGCACTTCCAGGACAACTTACATGTGGTCAACCGGGACCTCAATGAGCTGGAACGTCTGAGGAATCTGGTAGGCAAGCCA
TCTGAGAACCATCCTCTTCATAACAGTGGGCTGTTAAGCCTGGATCGTGTGCAGGACAAAACTCCTCTCTATAGTCAACT
CCTTCAAGCATATAAGTGGTCAAACAAGTTGCAGTACCATGCAGGACTAGCATCTGGCCTTTTAAATCAGCAGTCGTTGA
AGCGTTCCGCTAATCAGATGGGAGTATCTGCCAAACGTAGACCAAAGGCTCAGCCCACAACTCTTGTCCTACCACCTCAA
TATGTTGATGATGTGATCAGCCGCATTGACAGGATGTTTCCTGAAATGTCCATCCACTTATCCAGACCCAATGGAACATC
AGCAATGCTTCTGGTGACCTTGGGAAACGTGTTGAAAGTGATCGTCATCATGCGGAGCCTGTCCATTGATCGAACAATAG
CAAAGGGATATAACGAGAATGTCTACACAGAAGATGGCAAGCTTGATATATGGTCCAAATCCAACTATCAAGTATTCCAG
AAGGTGACAGACCACGCCACCACGGCCCTGCTCCACTATCAGCTGCCCCAGATGCTGGATGTCGTAGTCCGATCCTTCAT
GACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCATGCCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCC
CGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAG

Alignment

ORF - retro_ptro_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 84.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFQDNLHSVNRDLNEL
          MADVINV.VNLEAFSQAISAIQAL.SS.SRVFDCLKDGMRNKETLEGREKAFIAHFQDNLH.VNRDLNEL
Retrocopy MADVINVTVNLEAFSQAISAIQALHSSGSRVFDCLKDGMRNKETLEGREKAFIAHFQDNLHVVNRDLNEL

Parental  ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM
          ERL.NLVGKPSENHPLHNSGLLSLD.VQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM
Retrocopy ERLRNLVGKPSENHPLHNSGLLSLDRVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM

Parental  GVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVVMRSLFID
          GVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLG.VLKVIV.MRSL.ID
Retrocopy GVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGNVLKVIVIMRSLSID

Parental  RTIVKGYNENVYTEDGKLDIWSKSNYQVFQK
          RTI.KGYNENVYTEDGKLDIWSKSNYQVFQK
Retrocopy RTIAKGYNENVYTEDGKLDIWSKSNYQVFQK

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	3.02 RPM	9.44 RPM
SRP007412_cerebellum	1.47 RPM	8.35 RPM
SRP007412_heart	0.58 RPM	4.78 RPM
SRP007412_kidney	1.60 RPM	5.39 RPM
SRP007412_liver	1.05 RPM	4.58 RPM
SRP007412_testis	1.79 RPM	11.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_87 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_87 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_87 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3342
Gorilla gorilla	retro_ggor_130
Pongo abelii	retro_pabe_109

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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 ,