RetrogeneDB ID: retro_pabe_3574

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:13319482..13320061(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB19
• Ensembl ID: ENSPPYG00000018056
• Aliases: None
• Description: RAB19, member RAS oncogene family [Source:HGNC Symbol;Acc:19982]

Sequence

>retro_pabe_3574
GACGAGCAGTACGATTTCCTCTTCAAGCTGGTGCTGGTGGGCGACGCAAGCGTGGGCAAGACGTGCATGGTGCAGCGCTT
CAAGACCGGCGCCTTCTTGGAGGGCCAGGGAAGCACCATCGGCGTCGACTTCACCATGAAGATGCTGGAGATCCAGGGCA
AGCGGGTCAAGCTGCAGATCTGGGACACGGCCGGCCAGAAGTGGTTCCGCACCATCACCCAGAGATATTACCGCAGTGCC
AATGGGGCCATCCTTGCCTACGACATCACCAAGAGGAGCTCCTTCTTGTCGGTGCCTCACTGGATTGAGGATGTGAGGAA
GTACACGGGTTCCAACATTGTGCAGCTGCTGATCAGGAACAAGTCAGACCTCAGCGAGCTTCGGGAGGTCTCCCTGGCTG
AGGCACAGAGCCTGGCTGAGCACTATGAAATCCTGTGTGCCATTGAGACGTCTGCCAAGGACTCGAGCAAGGTGGAGGAG
GCCTTCCTGAGGGTGGCCACGGAGCTCATCATGCGGCACGGGAGCCCCCTGTTCAGCGAGAAGAGCCCCGACCACATACA
GCTGAACAGCAAGGACATC

Alignment

ORF - retro_pabe_3574 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.81 %
• Parental protein coverage: 88.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DENFDYLFKIILIGDSNVGKTCVVQHFKSGVYTETQQNTIGVDFTVRSLDIDGKKVK-QVWDTAGQERFG
          DE..D.LFK..L.GD..VGKTC.VQ.FK.G...E.Q..TIGVDFT...L.I.GK.VK.Q.WDTAGQ..F.
Retrocopy DEQYDFLFKLVLVGDASVGKTCMVQRFKTGAFLEGQGSTIGVDFTMKMLEIQGKRVKLQIWDTAGQKWFR

Parental  SITQRY-RSAQAAIIAYDITRRSTFESIPHWIHEIEKYGGATVVIILTGNKCDLWEKRHVLFEDACTLAE
          .ITQRY.RSA..AI.AYDIT.RS.F.S.PHWI....KY.G...V..L..NK.DL.E.R.V....A..LAE
Retrocopy TITQRYYRSANGAILAYDITKRSSFLSVPHWIEDVRKYTGSNIVQLLIRNKSDLSELREVSLAEAQSLAE

Parental  KYGLLAVLETSAKESKNIDEVFVLMAKELIARNSLHLYGESASNGLPLDSSPV
          .Y..L...ETSAK.S....E.F...A.ELI.R....L..E.......L.S...
Retrocopy HYEILCAIETSAKDSSKVEEAFLRVATELIMRHGSPLFSEKSPDHIQLNSKDI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.00 RPM
SRP007412_kidney	0.10 RPM	0.43 RPM
SRP007412_liver	0.18 RPM	0.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3574 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000000128	1 retrocopy	retro_pabe_3321,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pongo abelii	ENSPPYG00000018056	1 retrocopy	retro_pabe_3574 ,