RetrogeneDB ID: retro_hsap_2708

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:133209792..133210404(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000214301
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAF1
• Ensembl ID: ENSG00000179632
• Aliases: None
• Description: MAF1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24966]

Sequence

>retro_hsap_2708
CACATACTGAAGGCTCTCTCCCCATCCCAGACCTCAGGCCTCAGCCCCAGCAGCCTGAGCAAGAACCAAGGTGGCAAGGA
CAAGGGCCCCCCTCAGGGACAAGTGCAATTGCAAGACCCTCTTCCACTTGATTGTCATGCTCAGCGAGTCCTTTCAGGCC
TGACTATGACCTCAGCACAGCCCGCAGCCATGGGTTCAGCCGGAAGCCCAGCCTCAGGTGGGTGGTGAATGCAGTCAACC
GCAGTCTGTTCTCAGCTGCGTGGGGGGACATCAAGGTCCTAGAACACAGCTGTGGAACACAGTGGATGAGGAGATCCACC
TGGCTTAATGAGACACCCACAGCTATAACCCAGACATGGACCCAGATGCCTTCAGAGAAGAAGATACCCTCTGGTCCTTC
AACTACTTCTTCTACAACAAAGGGCTCAAGCAAATTGTTTTCTTCAGCCACCGCTCCATTAGCAGCTCCACCTGCACACC
CTCAGAGGCAGGCAACGAGATGGACCTGGAACTGGGGGAAGAGGAGGAAGAGAAAGGAAGCAGAGGTGGAGGCAGTGAGG
GTGGGGCCGAAGAGACCAGACCAAGGAGGACAGGTTCCCAGTGATTTGTATG

Alignment

ORF - retro_hsap_2708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.33 %
• Parental protein coverage: 79.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HVLEALSPPQTSGLSPSRLSKSQGGEEEGP-LSDKCSRKTLFYLIATLNESF-RPDYDFSTARSHEFSRE
          H.L.ALSP.QTSGLSPS.LSK.QGG...GP.L.DKC..KTLF.LI..L.ESF.RPDYD.STARSH.FSR.
Retrocopy HILKALSPSQTSGLSPSSLSKNQGGKDKGP>LRDKCNCKTLFHLIVMLSESF>RPDYDLSTARSHGFSRK

Parental  PSLSWVVNAVNCSLFSAVREDFKDL-KPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSLWSFNYFF
          PSL.WVVNAVN.SLFSA...D.K.L...QLWN.VDEEI.LA..D..SYNPD.D.D.F.E...LWSFNYFF
Retrocopy PSLRWVVNAVNRSLFSAAWGDIKVL<RTQLWNTVDEEIHLA**DTHSYNPDMDPDAFREEDTLWSFNYFF

Parental  YNKRLKRIVFFSCRSISGSTYTPSEAGNELDMELGEEEVEEESRSGGS--GAEET-STMEEDRVPVICI
          YNK.LK.IVFFS.RSIS.ST.TPSEAGNE.D.ELGEEE.E..SR.GGS..GAEET..T.E.DR.PVIC.
Retrocopy YNKGLKQIVFFSHRSISSSTCTPSEAGNEMDLELGEEEEEKGSRGGGSEGGAEET<QTKE-DRFPVICM

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	0.00 RPM	97.14 RPM
bodymap2_adrenal	0.08 RPM	84.64 RPM
bodymap2_brain	0.00 RPM	24.92 RPM
bodymap2_breast	0.00 RPM	71.30 RPM
bodymap2_colon	0.00 RPM	145.71 RPM
bodymap2_heart	0.00 RPM	72.92 RPM
bodymap2_kidney	0.00 RPM	56.79 RPM
bodymap2_liver	0.00 RPM	18.69 RPM
bodymap2_lung	0.00 RPM	77.41 RPM
bodymap2_lymph_node	0.20 RPM	89.19 RPM
bodymap2_ovary	0.00 RPM	72.58 RPM
bodymap2_prostate	0.00 RPM	113.83 RPM
bodymap2_skeletal_muscle	0.00 RPM	140.90 RPM
bodymap2_testis	0.23 RPM	86.31 RPM
bodymap2_thyroid	0.19 RPM	98.19 RPM
bodymap2_white_blood_cells	0.00 RPM	78.77 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_2708 in 9 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	3:133209657..133210174
ENCFF002CIO	POLR2A	3:133209621..133210165
ENCFF002CPH	POLR2A	3:133209651..133210041
ENCFF002CQA	POLR2A	3:133209645..133210215
ENCFF002CQC	POLR2A	3:133209666..133210146
ENCFF002CQG	POLR2A	3:133209682..133210206
ENCFF002CQK	POLR2A	3:133209591..133210081
ENCFF002CQM	POLR2A	3:133209785..133210265
ENCFF002CQO	POLR2A	3:133209682..133210212

EST

No EST(s) were mapped for retro_hsap_2708 retrocopy.

TSS

No TSS is located nearby retro_hsap_2708 retrocopy 5' end.

Lab

retro_hsap_2708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2708 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1829
Pongo abelii	retro_pabe_2259
Macaca mulatta	retro_mmul_1537

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021450	1 retrocopy	retro_cjac_2111,
Homo sapiens	ENSG00000179632	1 retrocopy	retro_hsap_2708 ,
Macaca mulatta	ENSMMUG00000007155	1 retrocopy	retro_mmul_1537,
Nomascus leucogenys	ENSNLEG00000010478	1 retrocopy	retro_nleu_1580,
Pongo abelii	ENSPPYG00000018963	1 retrocopy	retro_pabe_2259,
Pan troglodytes	ENSPTRG00000020681	1 retrocopy	retro_ptro_1829,