RetrogeneDB ID: retro_pabe_1626

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:20138845..20139167(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000019351
• Aliases: None
• Description: None

Sequence

>retro_pabe_1626
AGAATGAATGAGGTACTAGCAGCAGTCTGCACCAAGCTTCTACAGACATAATGCGTCAAATGTTTACTCTCCATTTTTAC
TACAAGGCCAGTCCAAGAGTTACCTTGTGTTGAAAATCTTAATAGTGTAGGTCTCAACAGAGGACATATTATGAGAGAAA
ACTTAAGGATCCCTACCTCATACCCAGAGACCTCAAATAGCAGCATGAACTACTCAACCAAGACTCAGCCAGATTGGATA
GAAAAAAATAACTACAGAAGTAAAAAATGTTGTTGCTGAATTGGAAATTAGCTCTCATATGGTTTCTTCTGTAGAATCCA
CT

Alignment

ORF - retro_pabe_1626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.46 %
• Parental protein coverage: 63.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSNKKIAVISTKLLMEKERMKYFLSTLPTRPDPELPCVENLNSIGLNRKYIPKTPIRIPTSNPQTSNNCK
          R.N...A...TKLL......K..LS...TRP..ELPCVENLNS.GLNR..I.....RIPTS.P.TSN...
Retrocopy RMNEVLAAVCTKLL-QT*CVKCLLSIFTTRPVQELPCVENLNSVGLNRGHIMRENLRIPTSYPETSNSSM

Parental  NSLTEMEPDCVE-QIITETKKTFAVLGTCSHLLSSLEST
          N..T...PD..E..I.TE.K...A.L...SH..SS.EST
Retrocopy NYSTKTQPDWIE>KITTEVKNVVAELEISSHMVSSVEST

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	0.28 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	0.00 RPM
SRP007412_kidney	0.07 RPM	0.00 RPM
SRP007412_liver	0.06 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1626 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1626 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000019351	1 retrocopy	retro_pabe_1626 ,