RetrogeneDB ID: retro_ptro_2362

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:73602383..73603111(+)
• Located in intron of: ENSPTRG00000018341

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSPTRG00000020505
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_ptro_2362
ATGGCGGGGTACGACTTAACTACTCGCATCACGCACCTTTTGGATCGGCATCTAGTCTTTCCGCTCCTTGAGTTTCTCTC
TGTAAAGGAGATATATAAAGAAAAGGAATTATTACAAGGTAAATTGGACCTTCTTAGTGATGCCAACATGGTAGACTTTG
CTATGGATGCATACAAAAACCTTTATTCTGATGATATTCCTCATGCTTTGAGAGAGAATAGAACTACAGTTGTTGCACAA
CTGAAACAGCTTCAGGCAGAAACAGAACTAATCGTGAAAATGTTTGAAGATCCAGAAACGACAAGGCAAATGCGGTCAAC
CAGGGATGGTAGGATGCTCTTTGACTACCTGGCGGACAAGCATGGTTTTAGGCAGGAGTATTTAGATACATTCTACACAT
ATGCAAAATTCCAGTATGAATGTGGGAATTACTCAGGAGCAGCAGAATATCTTTATTTTTTCAGAGTGTTGGTTCCAGCA
ACAGACAGAAATGCTGTAAGTTCACTCTGGGGAAAGCTGGCCTCTGAAATCTTACAGCAGAATTGGGATGCAGACATGGA
AGACCTTACATGGTTAAAAGAGACCATAGATAATAATTCTGTGAGTTCTCCACTCCAGTCTCTTCAGCAGAGAGCATGGC
TCGTTCACTGGTCTCTGTTTTCTTCAATCACCCCAAAGGTTGTGATAATATTGTTGATCTCTTCCTTTACCAGCCACAGT
ATCTTAAT

Alignment

ORF - retro_ptro_2362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.53 %
• Parental protein coverage: 54.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHAL
          MA.YDLTTRI.H.LDRHLVFPLLEFLSVKEIY.EKELLQGKLDLLSD.NMVDFAMD.YKNLYSDDIPHAL
Retrocopy MAGYDLTTRITHLLDRHLVFPLLEFLSVKEIYKEKELLQGKLDLLSDANMVDFAMDAYKNLYSDDIPHAL

Parental  REKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTRDGRMLFDYLADKHGFRQEYLDTLYRYAKFQYE
          RE.RTTVVAQLKQLQAETE.IVKMFEDPETTRQM.STRDGRMLFDYLADKHGFRQEYLDT.Y.YAKFQYE
Retrocopy RENRTTVVAQLKQLQAETELIVKMFEDPETTRQMRSTRDGRMLFDYLADKHGFRQEYLDTFYTYAKFQYE

Parental  CGNYSGAAEYLYFFRVLXXXXXXXXXSSLWGKLASEIL-QNWDAAMEDLTRLKETIDNNSVSSPLQSLQQ
          CGNYSGAAEYLYFFRVL.........SSLWGKLASEIL.QNWDA.MEDLT.LKETIDNNSVSSPLQSLQQ
Retrocopy CGNYSGAAEYLYFFRVLVPATDRNAVSSLWGKLASEILQQNWDADMEDLTWLKETIDNNSVSSPLQSLQQ

Parental  RTWLIHWSLFVFFNHPK-GRDNIIDLFLYQPQYLN
          R.WL.HWSLF.....PK.G.DNI.DLFLYQPQYLN
Retrocopy RAWLVHWSLFSSIT-PK<GCDNIVDLFLYQPQYLN

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	2.61 RPM	26.60 RPM
SRP007412_cerebellum	4.12 RPM	61.91 RPM
SRP007412_heart	1.78 RPM	72.57 RPM
SRP007412_kidney	1.91 RPM	81.54 RPM
SRP007412_liver	0.92 RPM	45.57 RPM
SRP007412_testis	2.32 RPM	64.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2362 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2362 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3489
Gorilla gorilla	retro_ggor_2355

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362 ,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,