RetrogeneDB ID: retro_pabe_498

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:228886541..228886918(-)
• Located in intron of: ENSPPYG00000001995

Retrocopy information

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

Parental gene information

• Parental gene symbol: S100A10
• Ensembl ID: ENSPPYG00000000850
• Aliases: None
• Description: S100 calcium binding protein A10 [Source:HGNC Symbol;Acc:10487]

Sequence

>retro_pabe_498
CCGCACCNGCCACCCTCTACCCACCCGCCGCACGTACTAAGGAAAGGCGCACAGCCCGCCGCGCTCGCCTCTCTGCCCAG
CGTCCAGCTCGCCCAGCTCGCCCAGCTCTCCCAGCGTCCGCCACGCCTCAGCCAAGGCTTCAACAGACCACACCAAAATG
CCATCTCAAATGGAACACGCCATGGAAACCATGATGTTTACATTTCACAAATTCGCTGGGGATAAAGGCTACTTAACAAA
GGAGGACCTGAGAGTACTCATGGAAAAGGAGTTCCCTGGATTTTTGGAAAATCAAAAAGACCCTCTGGCTGTGGACAAAA
ATAATGAAGGACCTGGACCAGTGCAGAGATGGCAAAGTGGGCTTCCAGAGCTTCTTT

Alignment

ORF - retro_pabe_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.1 %
• Parental protein coverage: 54.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAPPPSTHQPHVLRK-AHS---SPRSPLRPASSSPSSPSVRRASVKASTDHTKMPSQMEHAMETMMFTFH
          P..PPSTH.PHVLRK.AHS...SP..P............VR.AS.KASTDHTKMPSQMEHAMETMMFTFH
Retrocopy PHXPPSTHPPHVLRK>AHSPPRSPLCPAXXXXXXXXXXXVRHASAKASTDHTKMPSQMEHAMETMMFTFH

Parental  KFAGDKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDK-IMKDLDQCRDGKVGFQSFF
          KFAGDKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDK.IMKDLDQCRDGKVGFQSFF
Retrocopy KFAGDKGYLTKEDLRVLMEKEFPGFLENQKDPLAVDK>IMKDLDQCRDGKVGFQSFF

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	33.51 RPM
SRP007412_cerebellum	0.00 RPM	7.78 RPM
SRP007412_heart	0.00 RPM	22.79 RPM
SRP007412_kidney	0.00 RPM	50.98 RPM
SRP007412_liver	0.00 RPM	27.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_498 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000000850	3 retrocopies	retro_pabe_1455, retro_pabe_1731, retro_pabe_498 ,