RetrogeneDB ID: retro_pabe_1259

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:64420049..64420250(+)
• Located in intron of: ENSPPYG00000006585

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000006176
• Aliases: None
• Description: None

Sequence

>retro_pabe_1259
AGACCAGCCTGGCCAACATGGCAAAACCCCGTCTCTACTAAAAAATACAAAAATTAGCTAGGCATGGTGGCAGGCACCTG
TAATCCCAGCTACTTGGGAGGCTGAGGCAAGAATTACTTGAACCTGGGAGATGGAGGGTGCAGTGAGCCGAGATTGCACC
ACTACACTCCAACACAGCAAGCAGCACAGCAAGACTCCGTG

Alignment

ORF - retro_pabe_1259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KPAWPTIK-PVSTT-NTKISRAWWCVPVIPATREAE-GENPWNPGGEGCSEPRSCHCTPA-WATQQDSV
          .PAWPT...PVST..NTKIS.AWW..PVIPAT.EAE.G.N..N.G..GCSEPR..H.TP...A.QQDSV
Retrocopy RPAWPTWQNPVSTK>NTKIS*AWWQAPVIPATWEAE<GKNYLNLGDGGCSEPRLHHYTPTQQAAQQDSV

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	0.33 RPM
SRP007412_cerebellum	0.00 RPM	0.24 RPM
SRP007412_heart	0.03 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.07 RPM
SRP007412_liver	0.00 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1259 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1259 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020103	14 retrocopies	retro_cjac_3387, retro_cjac_3463, retro_cjac_3466, retro_cjac_3471, retro_cjac_3522, retro_cjac_3527, retro_cjac_3574, retro_cjac_3575, retro_cjac_3586, retro_cjac_3699, retro_cjac_3705, retro_cjac_3737, retro_cjac_3750, retro_cjac_3753,
Pongo abelii	ENSPPYG00000006176	2 retrocopies	retro_pabe_1259 , retro_pabe_739,