RetrogeneDB ID: retro_nleu_1189

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397284.1:21660962..21661697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSNLEG00000014333
• Aliases: None
• Description: None

Sequence

>retro_nleu_1189
ATGAACAATAAATCTGATGCTTTGAAAGATGACAACAATAGGGACCATGATCAGAATGAAGAAAGCAGCACACAGAAAGA
TACTGAGAAAGAAAAAACACAATGGGGATAAGAATAAGAGCAGTAACAAGAGGAAGGCTGTTGTCCCTGGACAGACAGCA
CATCCCCTGCAGTACAACTACACTTTCTGGTACTCCAGGAGAACCCCTGGCTGTCCCACCAGCTCACAGAGTTATGAATA
GAATATCAAACAGTTTGGCACCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTAATAGCCACATGGTATGTCCAAAGGATC
TGACAGGACACAGTGACTTCCATCTCTTCAAAGAAGGAATTAAATCCATGTGGGAGGATAATGCATATAAAAATGGTGAC
AAGAGGATTACTTGGCTGTGGAAGGGCTTGATCTCCCATTGCTAGGAGAATCTCATTTTGGCCGTATTGGGGGAACGGTT
CATGGTTGGGGAGGAGATCTGTGGGGCTGTGGTCTCTCTTCACTTTCAAGAGGACATTATTTCAATATGGAAAAGACTGC
CAGTGACCAAGCAACCACAGCCTGAATCCGGGATACACTTCGGCGAGTGCTTAACCTATCTCCCAACACCATTATGAAAT
ACAAAACTCACACTGACAGCATCAAAACGCCAGGCAGCCTGGGCTCCCAAAAGCTCCTTTATGAAAACCTCTGGAAGCTG
TGGTTGAATGGGCCA

Alignment

ORF - retro_nleu_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTE-RDKNQTSSKRKAVVPGPAEHPLQYNYTFWYSRRTP
          MNNK.DALKDD...DHDQNEE.STQKD.EKEKT...DKN..S.KRKAVVPG...HPLQYNYTFWYSRRTP
Retrocopy MNNKSDALKDDNNRDHDQNEESSTQKDTEKEKTQ>GDKNKSSNKRKAVVPGQTAHPLQYNYTFWYSRRTP

Parental  GRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRL
          G.PTSSQSYE.NIKQ.GTFASVEQFWRF.SHMV.P.DLTGHSDFHLFKEGIK.MWED.A.KNG.K.I..L
Retrocopy GCPTSSQSYE*NIKQFGTFASVEQFWRFNSHMVCPKDLTGHSDFHLFKEGIKSMWEDNAYKNGDKRITWL

Parental  RKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIW-NKTASDQATTARIRDTLRRVLNLPP
          .KGL.S.C.ENLILA.LGE.FMVGEEICGAVVS..FQEDIISIW..KTASDQATTA.IRDTLRRVLNL.P
Retrocopy WKGLISHC*ENLILAVLGERFMVGEEICGAVVSLHFQEDIISIW<EKTASDQATTA*IRDTLRRVLNLSP

Parental  NTIMEYKTHTDSIKMPGRLGPQRLLFQNLWKPRLNVP
          NTIM.YKTHTDSIK.PG.LG.Q.LL..NLWK..LN.P
Retrocopy NTIMKYKTHTDSIKTPGSLGSQKLLYENLWKLWLNGP

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_1189 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189 ,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,