RetrogeneDB ID: retro_ptro_1829

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:136993197..136993806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAF1
• Ensembl ID: ENSPTRG00000020681
• Aliases: None
• Description: None

Sequence

>retro_ptro_1829
CACGTACTGAAGGCTCTCTCCCCATCCCAGACCTCAGGCCTCAGCCCCAGCAGTCTGAGCAAGAACCAAGGTGGCAAGGA
CAAGGGCCCCCCTCAGGGACAAGTGCAATTGCAAGACCCTCTTCCACTTGATTGTCATGCTCAGCGAGTCCTTTCAGGCC
TGACTATGACCTCAGCACAGCCCGCAGCCATGGGTTCAGCCGGAAGCCCAGCCTCAGGTGGGTGGTGAATGCAGTCAACT
GCAGTCTGTTCTCAGCTGCGTGGGGGGACATCAAGGTCCTAGAACACAGCTGTGGAACACAGTGGATGAGGAGATCCACC
TGGCTTAATGAGACACCCACAGCTATAACCCAGACATGGACCCAGACGCCTTCAGAGAAGAAGATACCCGCTGGTCCTTC
AACTACTTCTACAACAAAGGGCTCAAGCAAATTGTTTTCTTCAGCCACCGCTCCATTAGCAGCTCCACCTGCACACCCTC
AGAGGCAGGCAACGAGATGGACCTGGAACTGGGGGAAGAGGAGGAAGAGAAAGGAAGCAGAGGTGGAGGCAGTGAGGGTG
GGGCCGAAGAGACCAGACCAAGGAGGACAGGTTCCCAGTGATTTGTATG

Alignment

ORF - retro_ptro_1829 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
          HVL.ALSP.QTSGLSPS.LSK.QGG...GP.L.DKC..KTLF.LI..L.ESF.RPDYD.STARSH.FSR.
Retrocopy HVLKALSPSQTSGLSPSSLSKNQGGKDKGP>LRDKCNCKTLFHLIVMLSESF>RPDYDLSTARSHGFSRK

Parental  PSLSWVVNAVNCSLFSAVREDFKDL-KPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSLWSFNYFF
          PSL.WVVNAVNCSLFSA...D.K.L...QLWN.VDEEI.LA..D..SYNPD.D.D.F.E....WSFNYF.
Retrocopy PSLRWVVNAVNCSLFSAAWGDIKVL<RTQLWNTVDEEIHLA**DTHSYNPDMDPDAFREEDTRWSFNYF-

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	45.29 RPM
SRP007412_cerebellum	0.04 RPM	51.26 RPM
SRP007412_heart	0.00 RPM	43.89 RPM
SRP007412_kidney	0.00 RPM	84.34 RPM
SRP007412_liver	0.00 RPM	39.28 RPM
SRP007412_testis	0.21 RPM	65.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1829 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1829 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2708
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 ,