RetrogeneDB ID: retro_pabe_253

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:70643619..70644219(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERPINA5
• Ensembl ID: ENSPPYG00000006108
• Aliases: None
• Description: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5 [Source:HGNC Symbol;Acc:8723]

Sequence

>retro_pabe_253
GCTAAGTGGGAGACAAGCTTCAACCACAAAGGCACCCAAGAGCAGGACTTCTACGTGACCTCGGAGACTGTGGTCCGGGT
ACCCATGATGAGCCGCGAGGATTAGTATCACTACCTCCTGGACCGGAACCTCTCCTGCAGGGTGGTGGGGGTCCCCTACC
AAGGCAATGCCACAGCTTTGTTCATTCTCCCCAGTGAGGGAAAGATGCAGCAGGTGGAGAATGGACTGAGTGAGAAAACG
CTGAGGAAGTGGCTTAAGATATTCAAAAAGAGGCAGCTCGAGCTTTGCCTTCCCAAATTCTCCATTGAGGGCTCCTATCA
GCTGGAGAAAGTCCTCCCCAAGCTGGGGATCAGTAACGTCTTCACCTCCCATGCTGATCTGTCTGGCATCAGCAACCACT
CAAATATCCAGGTGTCTGAGATGGTGCACAAAGCTGTGGTGGAGGTGGATGAGTCGGGAACCAGAGCAGCGGCAGCCACG
GGGACAATCTTCACATTCAGGTCGGCCCACCTGAACTCTCAGAGGATAGTGTTCAACAGGCCCTTTCTGATGTTCATTGT
GGATAACAATATCCTCTTCCTTGGCAAAGTGAACCGCCCC

Alignment

ORF - retro_pabe_253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.5 %
• Parental protein coverage: 53.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKWETSFNHKGTQEQDFYVTSETVVRVPMMSREDQYHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ
          AKWETSFNHKGTQEQDFYVTSETVVRVPMMSRED.YHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ
Retrocopy AKWETSFNHKGTQEQDFYVTSETVVRVPMMSRED*YHYLLDRNLSCRVVGVPYQGNATALFILPSEGKMQ

Parental  QVENGLSEKTLRKWLKMFKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE
          QVENGLSEKTLRKWLK.FKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE
Retrocopy QVENGLSEKTLRKWLKIFKKRQLELCLPKFSIEGSYQLEKVLPKLGISNVFTSHADLSGISNHSNIQVSE

Parental  MVHKAVVEVDESGTRAAAATGTIFTFRSARLNSQRIVFNRPFLMFIVDNNILFLGKVNRP
          MVHKAVVEVDESGTRAAAATGTIFTFRSA.LNSQRIVFNRPFLMFIVDNNILFLGKVNRP
Retrocopy MVHKAVVEVDESGTRAAAATGTIFTFRSAHLNSQRIVFNRPFLMFIVDNNILFLGKVNRP

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	0.66 RPM
SRP007412_cerebellum	0.00 RPM	0.24 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.10 RPM	36.26 RPM
SRP007412_liver	1.59 RPM	380.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_253 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000003691	2 retrocopies	retro_pabe_3459, retro_pabe_3514,
Pongo abelii	ENSPPYG00000006108	1 retrocopy	retro_pabe_253 ,