RetrogeneDB ID: retro_pabe_143

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:48321243..48321828(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000008438
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KRTAP4-7
• Ensembl ID: ENSPPYG00000008436
• Aliases: None
• Description: keratin associated protein 4-7 [Source:HGNC Symbol;Acc:18898]

Sequence

>retro_pabe_143
ATGGTCAACTCCTGTTGTGGCTCCGTATGCTCTGACCAAGGCTGTGGCCAAAACCTCTGCCAAGAGACCTGCTGCTGCCC
CAGCTGCTGCCAGACCACCTGCTGCAGGACCATCTGCTGTCGCCCCAGCTGCAGTGTGTCCAGCTGCTGCAAGCCCCAGT
GCTGCCAGTCTGTGTGCTGCCAGCCCACCTGCTGCCATCCCAGCTACTGCATCTCCAGCTGCTGTCGCCCCAGCTGCTGT
GTGTCCAGCTGCTGCAAGCCCCAGTGCTGCCAGTCTGTGTGCTGCCAGCCCACCTGCTGCCGCCCCAGCTGCTGCATCTC
CAGCTGCTGTCGCCCCAGCTGCTGTGTGTCCAGCTGCTGCAAGCCCCAGTGCTGCCAGTCTGTGTGCTGCCAGCCCACCT
GCTGCCGCCCCAGCTGCTGCATCTCCAGCTGCTGTCGCCCCAGCTGCTGTGAATCCAGCTGCTGCCACCCCTGCTGCTGC
CTGCGTCCAGTCTGTGGCCGAGTCTCCTGCCACACCACTTGCTATCGCCCAACCTGCGTCATTTCCACCTGCCCCCGCCC
CATGTGCTGTGCCTCCTCTTGCTGC

Alignment

ORF - retro_pabe_143 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNSCCGSVCSDQGCGQDLCQETCCRPSCCQTTCCRTTCYRPSCCVSSCCRPQCCQSVCCQPTCCRPSCC
          MVNSCCGSVCSDQGCGQ.LCQETCC.PSCCQTTCCRT.C.RPSC.VSSCC.PQCCQSVCCQPTCC.PS.C
Retrocopy MVNSCCGSVCSDQGCGQNLCQETCCCPSCCQTTCCRTICCRPSCSVSSCCKPQCCQSVCCQPTCCHPSYC

Parental  ETTCGRPRCCISSCCRPSCCVSSCCRPQCCQSVCCQPTCCRPSCCRPCCCLRPVCGRVSCHTTCYRPICV
          ...C.RP.CC.SSCC.P.CC.S.CC.P.CC...CC...CCRPSCC...CC....C..V.C..TC.RP.C.
Retrocopy ISSCCRPSCCVSSCCKPQCCQSVCCQPTCCRPSCCISSCCRPSCCVSSCCKPQCCQSVCCQPTCCRPSCC

Parental  ISSCPRPLCCASSCC
          ISSC.RP.CC.SSCC
Retrocopy ISSCCRPSCCESSCC

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_143 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000008436	1 retrocopy	retro_pabe_143 ,
Vicugna pacos	ENSVPAG00000003505	1 retrocopy	retro_vpac_18,