RetrogeneDB ID: retro_pabe_1774

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:23609..24132(+)
• Located in intron of: ENSPPYG00000010687

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E
• Ensembl ID: ENSPPYG00000014944
• Aliases: None
• Description: eukaryotic translation initiation factor 4E [Source:HGNC Symbol;Acc:3287]

Sequence

>retro_pabe_1774
TGGGCACTCTGGTTTTTTTAAAAAAGATAAAAGCAAAACTTGGCAAGCAAACCTGCCGCTGATCTCTAAGTTTGATCCTG
TTGACTTTTGGGCTCTGTACAACCATATCCAGTTGTCTAGTAATTTAATGTCTGGCTGTGACTACTCACTTTTTAATGAT
GGTGTTGAGCCCATGTGGGAAGATGAGAAAAACAAATGGGGAGGATGATGGCTAATTTACATTGAACAAACAGCAGAGAC
GAAGGGACCTCAATCACTTTTGGCTAAAGATTCTACTGTGCCTTATTGGAGAATCTTTTGATGACTCAGTGATGATATAT
GTGCAGCTGTTGTTAATGTTAGAGCTAAAGGTGATAAGATAGCAGTATGGACTACTGAATGTGAAAACAGAGAAGCTGTT
ACACATATAGAGAGGGTATACAAGGAAAGGTTAGGACTTCCTCCAAATATCGTGATTGGTTATCAGTCCCATGCAGACAC
AGCTACTAAAAACAGCTCCGCCACTAAAAATAGGTTTGTTGTT

Alignment

ORF - retro_pabe_1774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.39 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WALWFF-KNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGG
          WALWFF.K.DKSKTWQANL.LISKFD.V.DFWALYNHIQLSSNLM.GCDYSLF.DG.EPMWEDEKNK.GG
Retrocopy WALWFF>KKDKSKTWQANLPLISKFDPV-DFWALYNHIQLSSNLMSGCDYSLFNDGVEPMWEDEKNKWGG

Parental  RWLI-TLNKQQRRSDLDRFWLETLLCLIGESFDD-YSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHI
          .WLI.TLNKQQRR.DL..FWL..LLCLIGESFDD..SDD.C.AVVNVRAKGDKIA.WTTECENREAVTHI
Retrocopy *WLI>TLNKQQRRRDLNHFWLKILLCLIGESFDD<LSDDICAAVVNVRAKGDKIAVWTTECENREAVTHI

Parental  GRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV
          .RVYKERLGLPP.IVIGYQSHADTATK..S.TKNRFVV
Retrocopy ERVYKERLGLPPNIVIGYQSHADTATKNSSATKNRFVV

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	0.17 RPM	28.20 RPM
SRP007412_cerebellum	0.24 RPM	25.05 RPM
SRP007412_heart	0.12 RPM	15.80 RPM
SRP007412_kidney	0.17 RPM	24.43 RPM
SRP007412_liver	0.24 RPM	15.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1774 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1774 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_601

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009450	9 retrocopies	retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Callithrix jacchus	ENSCJAG00000007151	2 retrocopies	retro_cjac_1373, retro_cjac_2097,
Cavia porcellus	ENSCPOG00000005383	4 retrocopies	retro_cpor_1033, retro_cpor_1480, retro_cpor_169, retro_cpor_501,
Dasypus novemcinctus	ENSDNOG00000013712	5 retrocopies	retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Echinops telfairi	ENSETEG00000007347	3 retrocopies	retro_etel_1285, retro_etel_1449, retro_etel_499,
Homo sapiens	ENSG00000151247	4 retrocopies	retro_hsap_1843, retro_hsap_2409, retro_hsap_2894, retro_hsap_3935,
Gorilla gorilla	ENSGGOG00000004718	3 retrocopies	retro_ggor_1497, retro_ggor_2005, retro_ggor_2160,
Macropus eugenii	ENSMEUG00000011104	3 retrocopies	retro_meug_2087, retro_meug_2114, retro_meug_428,
Microcebus murinus	ENSMICG00000001482	1 retrocopy	retro_mmur_1195,
Myotis lucifugus	ENSMLUG00000005035	3 retrocopies	retro_mluc_1519, retro_mluc_24, retro_mluc_474,
Macaca mulatta	ENSMMUG00000011066	2 retrocopies	retro_mmul_1451, retro_mmul_601,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Mustela putorius furo	ENSMPUG00000002041	1 retrocopy	retro_mputfur_37,
Mus musculus	ENSMUSG00000028156	6 retrocopies	retro_mmus_1059, retro_mmus_1478, retro_mmus_1872, retro_mmus_2362, retro_mmus_3462, retro_mmus_868,
Oryctolagus cuniculus	ENSOCUG00000001456	3 retrocopies	retro_ocun_1760, retro_ocun_596, retro_ocun_810,
Otolemur garnettii	ENSOGAG00000001131	1 retrocopy	retro_ogar_259,
Pongo abelii	ENSPPYG00000014944	3 retrocopies	retro_pabe_1774 , retro_pabe_2396, retro_pabe_3244,
Pan troglodytes	ENSPTRG00000016301	4 retrocopies	retro_ptro_1159, retro_ptro_1386, retro_ptro_1957, retro_ptro_2672,
Rattus norvegicus	ENSRNOG00000013183	11 retrocopies	retro_rnor_1437, retro_rnor_1534, retro_rnor_1544, retro_rnor_1545, retro_rnor_1853, retro_rnor_1854, retro_rnor_2017, retro_rnor_2159, retro_rnor_653, retro_rnor_781, retro_rnor_783,
Sorex araneus	ENSSARG00000007821	1 retrocopy	retro_sara_285,
Ictidomys tridecemlineatus	ENSSTOG00000002230	5 retrocopies	retro_itri_1548, retro_itri_1549, retro_itri_1818, retro_itri_1819, retro_itri_1863,
Tarsius syrichta	ENSTSYG00000010862	3 retrocopies	retro_tsyr_1077, retro_tsyr_1442, retro_tsyr_2169,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,