RetrogeneDB ID: retro_pabe_3045

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:12031664..12032227(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNA11
• Ensembl ID: ENSPPYG00000009366
• Aliases: None
• Description: guanine nucleotide binding protein (G protein), alpha 11 (Gq class) [Source:HGNC Symbol;Acc:4379]

Sequence

>retro_pabe_3045
ACTCTGGAGTCCATGATGGCGTGTTGCCTGAGCGATGAGGTGAAGGAGTCCAAGCGGATCAACGCGGAGATCCAGAAGCA
GCTGCGGGGGACAAGCGCGACTCCCGGCGCCAGCTCAAGCTACTGCTGCTCCGCACAGGCGAGAGCGGGAAGAGCACCTT
CATCCAGCACATGCGCATCATCCATGGCGCCAGCTACTCGGAGGAGGACAAGCGGGGCTTCACCAAGCTCCTCTACCAGA
ACATTTTCACCTCCATGCAGGCCATGATCCGGGCCATGGAGACGCTGAAGATCCTCTACAAGTAGGAGCAGAACAAGGCC
ATTGCGCTCCTGATCCGAGAGGTGGACGTGGAGAAGGTGGCCACCTTTGAGCATCGGTACGTCAGCGCCATCAAGACCCT
GTGGGACGACCCCGGCATCCAGGAGTGCTACGACCGCAGGCGCGAGTACCAGCTCTCGGACTCGGCCAAGTACTGCGTGA
CCGACGCGGACTGCATCGCCACCTCGAGCTGCCTGCCCACCCGGCAGGACGTGCTGCGGGTCCTCGTGCCCACCACCGGC
ATC

Alignment

ORF - retro_pabe_3045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.77 %
• Parental protein coverage: 52.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLESMMACCLIDEVKESKRINAEIEKQLRR-DKRDARRELKLLLLGTGESGKSTFIKQMRIIHGAGYSEE
          TLESMMACCL.DEVKESKRINAEI.KQLR..DKRD.RR.LKLLLL.TGESGKSTFI..MRIIHGA.YSEE
Retrocopy TLESMMACCLSDEVKESKRINAEIQKQLRG<DKRDSRRQLKLLLLRTGESGKSTFIQHMRIIHGASYSEE

Parental  DKRGFTKLVYQNIFTAMQAMIRAMETLKILYKYEQNKANALLIREVDVEKVTTFEHQYVSAIKTLWEDPG
          DKRGFTKL.YQNIFT.MQAMIRAMETLKILYK.EQNKA.ALLIREVDVEKV.TFEH.YVSAIKTLW.DPG
Retrocopy DKRGFTKLLYQNIFTSMQAMIRAMETLKILYK*EQNKAIALLIREVDVEKVATFEHRYVSAIKTLWDDPG

Parental  IQECYDRRREYQLSDSAKYYLTDVDRIATSGYLPTQQDVLRVRVPTTGI
          IQECYDRRREYQLSDSAKY..TD.D.IATS..LPT.QDVLRV.VPTTGI
Retrocopy IQECYDRRREYQLSDSAKYCVTDADCIATSSCLPTRQDVLRVLVPTTGI

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	0.06 RPM	28.70 RPM
SRP007412_cerebellum	0.00 RPM	22.13 RPM
SRP007412_heart	0.09 RPM	11.65 RPM
SRP007412_kidney	0.00 RPM	21.11 RPM
SRP007412_liver	0.00 RPM	8.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3045 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088256	1 retrocopy	retro_hsap_3865,
Gorilla gorilla	ENSGGOG00000014995	3 retrocopies	retro_ggor_1760, retro_ggor_2603, retro_ggor_2604,
Macaca mulatta	ENSMMUG00000002961	1 retrocopy	retro_mmul_1605,
Pongo abelii	ENSPPYG00000009366	1 retrocopy	retro_pabe_3045 ,
Pongo abelii	ENSPPYG00000019311	1 retrocopy	retro_pabe_3536,