RetrogeneDB ID: retro_pabe_1596

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:43731598..43731940(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000008290
• Aliases: None
• Description: None

Sequence

>retro_pabe_1596
ATGGAGCCCCTGAACCAGCAAATGCACAAGCAGGTCCATGAGATCCATTCTCACATGGGACACTTGGAGACGGCAGACAA
GCAGTCTGTGCACTTAGTAGAAGGTGAAATCCAAGCAAGCACAGACCAGATATTCAGCCATCTAGGACGTCTGGAGATTT
TGTCCAGCAAGGAGCCCCCTAACAAAAGGCAGAATGCCAAACTTCGGGTTGACCAGTGTAAGTATGATGTTCAGCACCTG
CAGACTGCTCTCAGAAACTTCCAGCATCAGTGCTATGCAAGGGAGCAGCAGGAGGGACAGCAAGAAGAGCTTCTATCTCG
AACCTTCACCACTAACAATTCT

Alignment

ORF - retro_pabe_1596 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPLYQQTHKQVHEIQSRMGRLETADKQSVHIVENEIQASIDQIFSRLERLEILSSKEPPNKRQNAKLRV
          MEPL.QQ.HKQVHEI.S.MG.LETADKQSVH.VE.EIQAS.DQIFS.L.RLEILSSKEPPNKRQNAKLRV
Retrocopy MEPLNQQMHKQVHEIHSHMGHLETADKQSVHLVEGEIQASTDQIFSHLGRLEILSSKEPPNKRQNAKLRV

Parental  DQLKYDVQHLQTALRNFQHRRHAREQQERQREELLSRTFTTNDS
          DQ.KYDVQHLQTALRNFQH...AREQQE.Q.EELLSRTFTTN.S
Retrocopy DQCKYDVQHLQTALRNFQHQCYAREQQEGQQEELLSRTFTTNNS

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	52.19 RPM
SRP007412_cerebellum	0.00 RPM	40.61 RPM
SRP007412_heart	0.00 RPM	19.00 RPM
SRP007412_kidney	0.03 RPM	84.82 RPM
SRP007412_liver	0.09 RPM	38.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1596 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013419	1 retrocopy	retro_cfam_1351,
Felis catus	ENSFCAG00000028951	1 retrocopy	retro_fcat_678,
Myotis lucifugus	ENSMLUG00000002709	1 retrocopy	retro_mluc_752,
Pongo abelii	ENSPPYG00000008290	1 retrocopy	retro_pabe_1596 ,
Pan troglodytes	ENSPTRG00000009323	1 retrocopy	retro_ptro_1290,
Ictidomys tridecemlineatus	ENSSTOG00000016069	2 retrocopies	retro_itri_1790, retro_itri_270,