RetrogeneDB ID: retro_hsap_3342

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:79646842..79647775(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000248569
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED27
• Ensembl ID: ENSG00000160563
• Aliases: MED27, CRAP34, CRSP34, CRSP8, TRAP37
• Description: mediator complex subunit 27 [Source:HGNC Symbol;Acc:2377]

Sequence

>retro_hsap_3342
ATGGCGGACGTGATAAATGTCAGTGTGAACCTGGAGGCCTTTTCCCAGGCCATTAGTGCCATCCAGGCGCTGCGCTCCAG
CGTGAGCAGGTTGTTCGACTGCCTGAAGGATGGGATGCGGAACAAGGAGACGCTGGAGGGCCGGGAGAAGGCCTTCATTG
CGCACTTCCAGGACAACTTACATTCGGTCAACCGGGACCTCAATGAGCTGGAACGTCTGAGCAATCTGGTAGGCAAGCCA
TCTGAGAACCATCCTCTTCATAACAGTGGGCTGTTAAGCCTGGATCCTGTGCAGGACAAAACTCCTCTCTATAGTCAACT
CCTTCAAGCATATAAGTGGTCAAACAAGTTGCAGTACCATGCAGGACTAGCATCTGGCCTTTTAAATCAGTAGTCGTTGA
AGCGTTCCGCTAATCAGATGGGAGTATCTGCCAAAAGTAGACCAAAGGCTCAGCCCACAACTCTTGTCCTACCACCTCAA
TATGTTGATGATGTGATCAGCCGCATTGACAGGATGTTTCCTGAAATGTCCATCCACTTATCCAGACCCAATGGAACATC
AGCAATGCTTCTGGTGACCTTGGGAAAGGTGTTGAAAGTGATCGTCATCATGCGGAGCCTGTTCATTGATCGAACAATAG
TAAAGGGATATAACGAGAATGTCTACACAGAAGATGGCAAGCTTGATATATGGTCCAAATCCAACTATCAAGTATTCCAG
AAGGTGACAGACCACGCCACCACGGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGGATGTCGTAGTCCGATCCTTCAT
GACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCATGCCAGCACTGCGGGAAGTTTCTGCAGGACGGCCTTCCCC
CGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAG

Alignment

ORF - retro_hsap_3342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVINVSVNLEAFSQAISAIQALRSSVSRVFDCLKDGMRNKETLEGREKAFIAHFQDNLHSVNRDLNEL
          MADVINVSVNLEAFSQAISAIQALRSSVSR.FDCLKDGMRNKETLEGREKAFIAHFQDNLHSVNRDLNEL
Retrocopy MADVINVSVNLEAFSQAISAIQALRSSVSRLFDCLKDGMRNKETLEGREKAFIAHFQDNLHSVNRDLNEL

Parental  ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQQSLKRSANQM
          ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQ.SLKRSANQM
Retrocopy ERLSNLVGKPSENHPLHNSGLLSLDPVQDKTPLYSQLLQAYKWSNKLQYHAGLASGLLNQ*SLKRSANQM

Parental  GVSAKRRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVVMRSLFID
          GVSAK.RPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIV.MRSLFID
Retrocopy GVSAKSRPKAQPTTLVLPPQYVDDVISRIDRMFPEMSIHLSRPNGTSAMLLVTLGKVLKVIVIMRSLFID

Parental  RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAP
          RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAP
Retrocopy RTIVKGYNENVYTEDGKLDIWSKSNYQVFQKVTDHATTALLHYQLPQMPDVVVRSFMTWLRSYIKLFQAP

Parental  CQRCGKFLQDGLPPTWRDFRTLEAFHDTCRQ
          CQ.CGKFLQDGLPPTWRDFRTLEAFHDTCRQ
Retrocopy CQHCGKFLQDGLPPTWRDFRTLEAFHDTCRQ

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
bodymap2_adipose	0.44 RPM	7.39 RPM
bodymap2_adrenal	0.59 RPM	12.26 RPM
bodymap2_brain	0.28 RPM	10.13 RPM
bodymap2_breast	0.08 RPM	5.23 RPM
bodymap2_colon	0.02 RPM	5.63 RPM
bodymap2_heart	0.18 RPM	6.59 RPM
bodymap2_kidney	0.04 RPM	7.16 RPM
bodymap2_liver	0.19 RPM	3.87 RPM
bodymap2_lung	0.30 RPM	9.56 RPM
bodymap2_lymph_node	0.11 RPM	5.37 RPM
bodymap2_ovary	0.46 RPM	10.45 RPM
bodymap2_prostate	0.28 RPM	10.36 RPM
bodymap2_skeletal_muscle	0.27 RPM	9.60 RPM
bodymap2_testis	0.81 RPM	16.18 RPM
bodymap2_thyroid	0.51 RPM	9.32 RPM
bodymap2_white_blood_cells	0.00 RPM	10.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3342 was not detected

EST

1 EST(s) were mapped to retro_hsap_3342 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CN282021	79647414	79647573	100	159	0	159

TSS

No TSS is located nearby retro_hsap_3342 retrocopy 5' end.

Lab

retro_hsap_3342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3342 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_87
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.08 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.09 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.13 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.12 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.04 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).