RetrogeneDB ID: retro_pabe_1640

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:46379264..46379715(+)
• Located in intron of: ENSPPYG00000010107

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_1640
ATGGCAGATGATTTGGACTTCGAGACAAGAGATGCAGGGGCCTCGGCCTCCTTCCCAATGCAGTGCTCAGCATTATGTAA
CACTGGCTTCGTGGTGCTCAAAGCCTGGCCCCTGTAAAATCTTCGAGGTGTCTGCTTGGAAGACTGGCAAGCACGGCCAC
GCCAAGGTCCACCTGGTTGGTATTGACATCTTTACTGGGAAGAAATATAAAGATAACTGCCTGTCACCTTATAATGTGGG
TGTCCCCAACATCAAAAGGAATGAGTCCCAGCTGATTGGCATCCAGGAAGGTACCCCTCACTGCTCTAGGACAGCAGGGA
GGTGCCAGAGGACCTTCTTCGTCTGCCTGAGGAGACCTTGGCAAGGAGATGAGCAGAAGTACCGCTGTGGAGAAGAGACC
CTGATCACCGTGCTGTCTGCCATGACAGAGGAGGCACCTGTTGCAGTCAAG

Alignment

ORF - retro_pabe_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 98.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MADEIDFTTGDAGASSTYPMQCSALRKNGFVVLKG-RPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKY
          MAD..DF.T.DAGAS...PMQCSAL...GFVVLK...PCKI.E.S..KTGKHGHAKVHLVGIDIFTGKKY
Retrocopy MADDLDFETRDAGASASFPMQCSALCNTGFVVLKA>GPCKIFEVSAWKTGKHGHAKVHLVGIDIFTGKKY

Parental  EDICPSTHNMDVPNIKRNDYQLICIQDG-YLSLLTETGEVRED-LKLPE-GELGKEI-EGKYNAGEDVQV
          .D.C.S..N..VPNIKRN..QLI.IQ.G.Y.SLL....EV.ED.L.LPE.G.LGKE..E.KY..GE....
Retrocopy KDNCLSPYNVGVPNIKRNESQLIGIQEG<YPSLL*DSREVPEDLLRLPE<GDLGKEM<EQKYRCGEETLI

Parental  SVMCAMSEEYAVAIK
          .V..AM.EE..VA.K
Retrocopy TVLSAMTEEAPVAVK

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	0.66 RPM	2.27 RPM
SRP007412_cerebellum	1.09 RPM	1.95 RPM
SRP007412_heart	0.30 RPM	1.54 RPM
SRP007412_kidney	0.60 RPM	1.76 RPM
SRP007412_liver	0.21 RPM	0.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1640 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1640 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1640 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2004
Gorilla gorilla	retro_ggor_1448
Macaca mulatta	retro_mmul_1379

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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,