RetrogeneDB ID: retro_pabe_2409

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3_random:8517308..8517740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSPPYG00000029434
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma [Source:HGNC Symbol;Acc:3213]

Sequence

>retro_pabe_2409
CTGGCTGACATCACAGTTGTCTGCACCTTGTTGTGGCTCTATAAGCAGGTGCTGGAGCCTTCTTTCCACCAGCCTTTCTC
AGTAACAACCCTTGGCTCCTCACCTGCATTAACCAGACCCAGTTGTGGGCTGTCTTGGAATAAGTGAAACTGTGTGAGAA
GATGGCCCAGTTTGATGCTAAAAATTCTACAGACAGCCCGACTAAAAACGACACCCATGGAAAGGGAGAGGTTCATTAAA
AGAGAAGCAGATGCCTCAGGCTAAACAGAAACAGGAAAAAATGTGGCTTCCCTTGCTTCTGAGGAGGAGATGGATGAATG
TGAGCAGGCACTGGCTGCTGAGCCCAAGGCCAAGGGCCTCTTTGCTCAGCTGCTCGAGGGTACCTTTGTGTTGGGTGAAT
TTATACCCAAGTGCTCCAGTGAGGATACACTG

Alignment

ORF - retro_pabe_2409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.24 %
• Parental protein coverage: 61.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LADITVVCTLLWLYKQVLEPSFRQ-AFPNTNRWFLTCINQPQFRAVLGEVKLCEKMAQFDAKKFAETQPK
          LADITVVCTLLWLYKQVLEPSF.Q.AF...N.W.LTCINQ.Q..AVL..VKLCEKMAQFDAK.......K
Retrocopy LADITVVCTLLWLYKQVLEPSFHQ<AFLSNNPWLLTCINQTQLWAVLE*VKLCEKMAQFDAKNSTDSPTK

Parental  KDT-PRKEKGSREEKQKPQAERKEEK-KAAAPAPEEEMDECEQALAAEPKAKDPFAHLPKSTFVLDEFKR
          .DT.P.K..GS..EKQ.PQA..K.EK...A..A.EEEMDECEQALAAEPKAK..FA.L...TFVL.EF..
Retrocopy NDT<PWKGRGSLKEKQMPQAKQKQEK<NVASLASEEEMDECEQALAAEPKAKGLFAQLLEGTFVLGEFIP

Parental  KYSNEDTL
          K.S.EDTL
Retrocopy KCSSEDTL

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	205.63 RPM
SRP007412_cerebellum	0.00 RPM	127.19 RPM
SRP007412_heart	0.00 RPM	351.76 RPM
SRP007412_kidney	0.00 RPM	555.94 RPM
SRP007412_liver	0.00 RPM	381.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2409 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2409 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409 , retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,