RetrogeneDB ID: retro_pabe_1308

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:69387233..69387485(-)
• Located in intron of: ENSPPYG00000006609

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A2
• Ensembl ID: ENSPPYG00000014294
• Aliases: None
• Description: Eukaryotic translation initiation factor 5A-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R898]

Sequence

>retro_pabe_1308
GAAGATATTTGTCCTTCTATTCACAACATGGATGTTCCAAATATTCAGAGACATGATTATCAACTGATACGCATTCAAGA
TAGTTGCCTTTCCCTGCTGACAGAAGCTGATGGAGTTCCTGAGGATCTTAAACTGCCAGAAAGTGAACTAGGCAAATAAA
TACAAGGAAAATACAATGCAGGTGAAGATGTACAGGTGTCTGTCATGTGTGCAATGAGTGAAGAATATGCTGTAGCCATA
AAACCCTGCAAA

Alignment

ORF - retro_pabe_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 54.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMC
          EDICPS.HNMDVPNI.R.DYQLI.IQD..LSLLTE...V.EDLKLPE.ELGK.I.GKYNAGEDVQVSVMC
Retrocopy EDICPSIHNMDVPNIQRHDYQLIRIQDSCLSLLTEADGVPEDLKLPESELGK*IQGKYNAGEDVQVSVMC

Parental  AMSEEYAVAIKPCK
          AMSEEYAVAIKPCK
Retrocopy AMSEEYAVAIKPCK

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	2.27 RPM
SRP007412_cerebellum	0.00 RPM	1.95 RPM
SRP007412_heart	0.00 RPM	1.54 RPM
SRP007412_kidney	0.00 RPM	1.76 RPM
SRP007412_liver	0.00 RPM	0.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1308 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1308 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1591
Pan troglodytes	retro_ptro_1070

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005363	1 retrocopy	retro_chof_1016,
Cavia porcellus	ENSCPOG00000012594	1 retrocopy	retro_cpor_1060,
Dasypus novemcinctus	ENSDNOG00000014801	2 retrocopies	retro_dnov_1133, retro_dnov_268,
Homo sapiens	ENSG00000163577	1 retrocopy	retro_hsap_1591,
Loxodonta africana	ENSLAFG00000013225	1 retrocopy	retro_lafr_901,
Macropus eugenii	ENSMEUG00000007473	2 retrocopies	retro_meug_1619, retro_meug_641,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308 , retro_pabe_1640,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,