RetrogeneDB ID: retro_ptro_1070

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:69605400..69605862(-)
• Located in intron of: ENSPTRG00000007243

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A2
• Ensembl ID: ENSPTRG00000015621
• Aliases: None
• Description: None

Sequence

>retro_ptro_1070
ATGGTGTACGAAATTGATTTAACTACTGGAGATGCTGGGGCTTCCAGCACTTACCCTATGCAGTGCTCAACCTTGTGCAA
AAGTGGCTTCATGGTGTTCAAAGGACAACCATGCAAAATAGTGAAGATGTTAACTTCCAAAACTGGAAAACATGGTCATG
CCAAGGTTCACCTTGTTGGAATTGCTGTTTTCATGGGAAAAAAAGAAGAAGAAGATATTTGTCCTTCTATTCACAACGTG
GATGTTCCAAATATTCAGAGACATGATTATCAACTGATATGCATTCAAGATAGTTGCCTTTCCCTGCCGACAGAAGCTGA
TGAAGTTCCTGAGGATCTTAAACTGCCAGAAAGTGAACTAGGCAAATAAATACAAGGAAAATACAATGCAGGTGAAGATG
TACAGGTGTCTGTCATGTGTGCAGTGAGTGAAGAATATGCTGTAGCCATAAAACCCTGCAAA

Alignment

ORF - retro_ptro_1070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEIDFTTGDAGASSTYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYE
          M..EID.TTGDAGASSTYPMQCS.L.K.GF.V.KG.PCKIV.M.TSKTGKHGHAKVHLVGI..F.GKK.E
Retrocopy MVYEIDLTTGDAGASSTYPMQCSTLCKSGFMVFKGQPCKIVKMLTSKTGKHGHAKVHLVGIAVFMGKKEE

Parental  -DICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMC
          .DICPS.HN.DVPNI.R.DYQLICIQD..LSL.TE..EV.EDLKLPE.ELGK.I.GKYNAGEDVQVSVMC
Retrocopy EDICPSIHNVDVPNIQRHDYQLICIQDSCLSLPTEADEVPEDLKLPESELGK*IQGKYNAGEDVQVSVMC

Parental  AMSEEYAVAIKPCK
          A.SEEYAVAIKPCK
Retrocopy AVSEEYAVAIKPCK

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	9.21 RPM
SRP007412_cerebellum	0.00 RPM	5.27 RPM
SRP007412_heart	0.00 RPM	4.63 RPM
SRP007412_kidney	0.00 RPM	7.69 RPM
SRP007412_liver	0.00 RPM	3.50 RPM
SRP007412_testis	0.00 RPM	10.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1070 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1070 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1591
Pongo abelii	retro_pabe_1308

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 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,
Macaca mulatta	ENSMMUG00000022880	1 retrocopy	retro_mmul_2222,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Pan troglodytes	ENSPTRG00000008674	3 retrocopies	retro_ptro_1198, retro_ptro_442, retro_ptro_504,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070 ,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,
Tupaia belangeri	ENSTBEG00000000408	2 retrocopies	retro_tbel_1442, retro_tbel_4419,