RetrogeneDB ID: retro_pabe_133

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:22046940..22047306(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000017529
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018258
• Aliases: None
• Description: None

Sequence

>retro_pabe_133
ATGGCAACCTTCCCTGGCCAGGTTTCCACCTATTTCCCAGCAACCTGGGCAGGCCCAGGTCCTGCCACACACTGGCCTCT
TTACGCCCAGCTCATACCTCACAGTGGCCTCTCCAGGCCCAGCTCCTGTCCCGGGACATCATCTCCAGGCCCAAAACTTC
CTCAAGTTGGCCTCTCCAGGCCCAGTTGCTGCCTCCTGGCATCCTCTCCAGGCCTAGCTCTTCCTCCTGGCTGTATCTAC
AAGCCCAACTCCTGCCTCACAACAACCTTTTATGGCTCAGCTCCTNNNNNNNNNNAACAGCCTCTGCAGGCCCCGCTCTT
GCCTCTTAGCTCCCTCTCCAGACCCAACTCTTGCCTCACAGTGGCT

Alignment

ORF - retro_pabe_133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.98 %
• Parental protein coverage: 92.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATFPGQVPACLPAAWTGPGPISHW-LYTQLMPHGGLSRPSSCPGMSSPGLKLP-FSLSSPSYCLLAS-PG
          ATFPGQV....PA.W.GPGP..HW.LY.QL.PH.GLSRPSSCPG.SSPG.KLP...LS.PS.CLLAS.PG
Retrocopy ATFPGQVSTYFPATWAGPGPATHWPLYAQLIPHSGLSRPSSCPGTSSPGPKLPQVGLSRPSCCLLASSPG

Parental  PALPPGCVYRPGSCVTATALDSAPAQLLVAFGGPKLPQAKLCRPAFCLPVA
          .ALPPGC.Y.P.SC.T.T...SAP.........P.LP...L.RP..CL.VA
Retrocopy LALPPGCIYKPNSCLTTTFYGSAPXXXXQPLQAPLLPLSSLSRPNSCLTVA

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	0.11 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.09 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_133 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000000034	1 retrocopy	retro_mmul_1610,
Pongo abelii	ENSPPYG00000018258	4 retrocopies	retro_pabe_133 , retro_pabe_3119, retro_pabe_3126, retro_pabe_3236,