RetrogeneDB ID: retro_pabe_2259

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:135888248..135888826(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAF1
• Ensembl ID: ENSPPYG00000018963
• Aliases: None
• Description: MAF1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24966]

Sequence

>retro_pabe_2259
TCAGGCCTCAGCCCCAGCAGCCTGATCAAGAACCAAGGTGGCAAGGACGAGGGCCCCCTCAGGTACAAGTGCAATTGCAA
GACCCTCTTCCACTTGATTGTCATGCTCAGCGAGTCCTTTCAGGCCTGACTATAACCTCAGCACAGCCCGCAGCCATGGG
TTCAGCTGGAAGCCCAGCCTCAGCTGGGTGGTGAACGCAGTCAACTGCAGTCTGTTCTCAGCTGCGTGGGGGAACATCAA
GGTCCGAGAACACAGCTGCGGAACACAGTGGATGAGGAGATCCGCCTGGCTTAATGGGACACCTACAGCTATAACCCAGA
CATGGACCCAGACCCCTTCAGGGAAGAAGACACCCTCTGGTCCTTCAACTACTTCTTCTACAACAAAGGGCTCAAGCAAA
TTTTCTTCTTCAGCCACCGCTCCATTAGCAGCTCCACCTGCACACCCTTAGAGGCAGGCAACGAGATGGACCTGGAACTG
GGTGAAGAGGAGGAAGAGAAAGAAAGCAGAGGCAGAGGCAGTGAGGGTGGGGCCAAAGAGACCAGACCATGGAGGACAGG
TTCCCAGTGATTTGTATG

Alignment

ORF - retro_pabe_2259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGLSPSRLSKSQGGEEEGPLSDKCSRKTLFYLIATLNESF-RPDYDFSTARSHEFSREPSLSWVVNAVNC
          SGLSPS.L.K.QGG..EGPL..KC..KTLF.LI..L.ESF.RPDY..STARSH.FS..PSLSWVVNAVNC
Retrocopy SGLSPSSLIKNQGGKDEGPLRYKCNCKTLFHLIVMLSESF>RPDYNLSTARSHGFSWKPSLSWVVNAVNC

Parental  SLFSAVREDFKAL-KPQLWNAVDEEICLAECDIYSYNPDLDSDPFGEDGSLWSFNYFFYNKRLKRIVFFS
          SLFSA.....K.....QL.N.VDEEI.LA..D.YSYNPD.D.DPF.E...LWSFNYFFYNK.LK.I.FFS
Retrocopy SLFSAAWGNIKVR<RTQLRNTVDEEIRLA*WDTYSYNPDMDPDPFREEDTLWSFNYFFYNKGLKQIFFFS

Parental  CRSISGSTYTPSEAGNELDMELGEEEVEEESRSGGS--GAEET-STMEEDRVPVICI
          .RSIS.ST.TP.EAGNE.D.ELGEEE.E.ESR..GS..GA.ET..TM.EDR.PVIC.
Retrocopy HRSISSSTCTPLEAGNEMDLELGEEEEEKESRGRGSEGGAKET<QTM-EDRFPVICM

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	29.91 RPM
SRP007412_cerebellum	0.00 RPM	23.83 RPM
SRP007412_heart	0.00 RPM	31.94 RPM
SRP007412_kidney	0.00 RPM	43.06 RPM
SRP007412_liver	0.00 RPM	16.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2259 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2259 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2708
Pan troglodytes	retro_ptro_1829
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,