RetrogeneDB ID: retro_nleu_2371

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397348.1:3750708..3751853(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSNLEG00000017727
• Aliases: None
• Description: None

Sequence

>retro_nleu_2371
GACAAGTATCGAGATAGTTATGATTCAGACCGGTATCACGATGGGTATCGGGATGGGTATTGGGATGGCCCACACTGGGA
TATGGATTGATGTGGCAGCTGGGATCGCTATGATGACCAAGGCAGCAGAGACTATGATAGACGCTATGATTCCCAGATAG
GCAATGGCAGAAGGGCATTTGGCAGTGGGTGCCACAGGGATGATGACTATAGAGGAGGCGGGACTGGCTATGAAGACCAA
TAAGACAGACAGGATGATCAGTCATGGAGCTCCAGAGATGATTACTCTCGGGATGATTATATGGGTGATGATAGAGGTCC
CTCCCAAAGACCCAAACTGAATCTAAAGCCTCAGAGTGCTCCTAAGGAAGATGATTCCTCTGCTAGTACCTCCCAGTCCA
GTGGAGGTGCTTCTATCTTTGGAGGGGCAAAGCCCGTTGACACAGCTGCTAGAGAAAGAGAAGTAGAAGAACAGCTACAG
AAGGAACACGAGAAGTTGCAGCATCAGCTGGATGAGCCAGAACTAGAATGACGGCCTCGGGAGAGACACCCAAGCTGACA
AAGTGAAGAAACTCAGGAACGGGAACAGTTGAGGACAGGAAGTGAGTCATTGCAGACTGGGACCTCCGCCACATCCGGCA
GAAATGCACGAAGGAGAGTGAGTGAGAAGTCACTAGAAAATGAAACACTCAATAAGGAGGAAGACTGTCACTCTCCAACT
TCTAAACCTCTCAAACTTGATCAGCCCTTAAAGGAGAATGGTTGGGTGAAGTGAAGTTCTAACTCTCCTGCTCGATCTCA
GAGCTCAGACACAGAGCAGCAATCCCCTACAATTGGTGGGGTAAAGTAGCTCCAGCTCAACCATCTGAGTAAGGACTAGC
AAGGAAAAACGAAAATGAAGTAGATGGGATGAATATCCCAAAAGGCCAAACTGGGAACTCTAGCCATGGTCCAGGAGAGG
GAGGGAACAAAGACCACTTGAAGGAGTCAGATAGGAAAGATGACAAAAAGGATAAAGACTCCAGATCTGCACCTGAGCCA
AAGAAACCTGAGGAAAATCCAGCTTCCAAGTTCAGTTCTGCAAGGAAGTATGCTGCTCTCTCCATTGATGGTGAAGATGA
AAACGAGGGAGAAGATTAAGCTGAA

Alignment

ORF - retro_nleu_2371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.03 %
• Parental protein coverage: 64.54 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSFGDKYRDRYDSDRYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGSGYRRDDDY
          D...D.Y................P..DMD..G..DRYDD.GSRDYDR.YDS.IG.GRRAFGSG..RDDDY
Retrocopy DKYRDSYDSDXXXXXXXXXXXXXPHWDMD*CGSWDRYDDQGSRDYDRRYDSQIGNGRRAFGSGCHRDDDY

Parental  RGGGDRYEDRYDRRDDRSWSSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSTRAASIF
          RGGG..YED..DR.DD.SWSSRDDYSRDDY.....G....P....K....P.........S.ST...S..
Retrocopy RGGGTGYEDQ*DRQDDQSWSSRDDYSRDDYM----GDDRGPSQRPKLNLKPQSAPKEDDSSASTSQSS--

Parental  GGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGSESSQTGTST
          GGA......A.......R.....E.LQ......KL.....E.....R..E......S....E..Q..T..
Retrocopy GGAS-IFGGAKPVDTAAREREVEEQLQKEHE--KLQHQLDEPELE*RPRERHPS*QSEETQEREQLRTGS

Parental  TSGRSKSDQDARRRESEKSLENETLNKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPARSQ
          .S..........R.......E....N...........P.....PLK.....P.KEN.WVK.SSN.PARSQ
Retrocopy ESLQTGTSATSGRNARRRVSEKSLENETLNKEEDCHSPTS--KPLKL--DQPLKENGWVK*SSNSPARSQ

Parental  SSDTEQQSPTSGG-GKVAPAQPSEEGPARKDENKVDGMNVPKGQTGNSSRGPGDGGNKDHWKESDRKDGK
          SSDTEQQSPT.GG.GKVAPAQPSE.G.ARK.EN.VDGMN.PKGQTGNSS.GPG.GGNKDH.KESDRKD.K
Retrocopy SSDTEQQSPTIGG<GKVAPAQPSE*GLARKNENEVDGMNIPKGQTGNSSHGPGEGGNKDHLKESDRKDDK

Parental  KDQDYRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
          KD.D.RSAPEPKKPEENPASKFSSA.KYAALS.DGEDENEGED.AE
Retrocopy KDKDSRSAPEPKKPEENPASKFSSARKYAALSIDGEDENEGED*AE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2371 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371 , retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,