RetrogeneDB ID: retro_pabe_188

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:1459433..1459943(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000002906
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000020050
• Aliases: None
• Description: None

Sequence

>retro_pabe_188
ATGGGCTGCTGTGGCTGCTCCGGAGGCTGCGGTTCCGGCTGTGGGGGCTGTGGGGGATGTGGCTCTAGCTGCTGTGTGCC
TGTCTGCTGCTGCAAGCCTGTGTGCTGCTGTGTGCCAGCTTGTTCCTGCTCCAGCTGTGGCAAAGGGGGCTGTGGCTCTT
GTGGGGGCTCCAAGGGGGGCTGTGGCTCCTGTTGGGGGTCCAAGGGGGGCTGTGGCTCCTGTGGGGGATCCAAGGGGGAC
TGTGGCTCCTGTGGGGGGTCGAAGGGGGACTGTGGCTCCTTTGGGGGCTCGAAGGGGGGCTGTGGTTCTTATGGCTGCTC
CCAGTGCAGCTGCTGGAAGCCCTGCTGCTGCTCCTCAGGCTGTGGGTCATCCTGCTGCCAGTCCAGCTGCTGTAAGCCCT
GTAGCTGCTCCTCAGGCTGTGGATCATCCTGCTGCCAATCCAGCTGCTACAAGCCCTGCTGCTGTCAGTCCAGCTGCTGT
GTCCCCGTGTGCTGCCAGTGTAAGATCTGA

Alignment

ORF - retro_pabe_188 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 87.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCGGCGSGCGGCGSGCGSGCGGCGSSCCVPVCCCKPVCSCVPACSCSSCGSCGGSKGGCDSCGGSKGSCG
          GC.GC....GGCGSGCG.GCGGCGSSCCVPVCCCKPVC.CVPAC...SC.SCG..KGGC.SCGGSKG.CG
Retrocopy GCCGCS---GGCGSGCG-GCGGCGSSCCVPVCCCKPVCCCVPAC---SCSSCG--KGGCGSCGGSKGGCG

Parental  SCGGSKGGCGSCGGSKGGCGSSCGGSGSSCGGCGSS--CCVPICCCSCSSCGSYGGSKGGCGSCSCCQSS
          SC.GSKGGCGSCGGSKG.CG.SCGGS...CG..G.S...C....C..C.SC........GCGS.SCCQSS
Retrocopy SCWGSKGGCGSCGGSKGDCG-SCGGSKGDCGSFGGSKGGCGSYGCSQC-SCWKPCCCSSGCGS-SCCQSS

Parental  CCKPCCCSSGCGSSCCQSSCCKPCCSQSSCCVPVCCQCKI
          CCKPC.CSSGCGSSCCQSSC.KPCC.QSSCCVPVCCQCKI
Retrocopy CCKPCSCSSGCGSSCCQSSCYKPCCCQSSCCVPVCCQCKI

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	0.03 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_188 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000020050	1 retrocopy	retro_pabe_188 ,