RetrogeneDB ID: retro_nleu_1862

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397313.1:12981519..12981954(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS25
• Ensembl ID: ENSNLEG00000011797
• Aliases: None
• Description: None

Sequence

>retro_nleu_1862
ATGGTGATGAATTTCAAGTGGTTGTGGCAGTATCGCTTCCCGCCCTTTACATTACAGCTGAATGTGGCCACTTGGCAGAA
GCAGCTGGCCATGTGGTGTTCGTTGGTTCTGTCCATCTGCTGCCTGCACAAACAGTCCAGCATGATGGTGATGGATGCTC
AGGAGATCCTGCTCTTCAGCAACATCAAGCTGTGGAAGCTTCCTGTGGGACCAAGCCAGGTTGTATTAGAGGAACTGAGG
AAGAATGGGAACTTACAGTGGCTGGATAAGAGGAAGTCTAGTTTCCTAATCATGTGGCGGAGGCCAGAAGAATGGGGAAA
ACTCGTCTATCAGTGGGTCTCCAGGAGTGGCCAGAACAACTCCATACTTAGCCTGTATGAGCTGACCAATGGGGAAGACA
CAGAGAATGAGGTGTTCCATGGACTAAAGGAGGCC

Alignment

ORF - retro_nleu_1862 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 83.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNNVKLQRKLP
          M.M.F.W.WQYRFPPF.TLQ.NV.T.QKQLA.WCSLVLS.C.LHKQSSM.VM.AQE..LF.N.KL..KLP
Retrocopy MVMNFKWLWQYRFPPF-TLQLNVATWQKQLAMWCSLVLSICCLHKQSSMMVMDAQEILLFSNIKLW-KLP

Parental  VESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEE
          V...Q.VLEELRK.GNL.WLDK.KSSFLIMWRRPEEWGKL.YQWVSRSGQNNS...LYELTNGEDTE.E.
Retrocopy VGPSQVVLEELRKNGNLQWLDKRKSSFLIMWRRPEEWGKLVYQWVSRSGQNNSILSLYELTNGEDTENEV

Parental  FHGLDEA
          FHGL.EA
Retrocopy FHGLKEA

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_1862 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013276	1 retrocopy	retro_cjac_2959,
Homo sapiens	ENSG00000131475	1 retrocopy	retro_hsap_213,
Gorilla gorilla	ENSGGOG00000016041	1 retrocopy	retro_ggor_284,
Macropus eugenii	ENSMEUG00000011611	2 retrocopies	retro_meug_1247, retro_meug_1681,
Macaca mulatta	ENSMMUG00000002149	1 retrocopy	retro_mmul_406,
Nomascus leucogenys	ENSNLEG00000011797	1 retrocopy	retro_nleu_1862 ,
Ochotona princeps	ENSOPRG00000012574	1 retrocopy	retro_opri_1071,
Pongo abelii	ENSPPYG00000008377	1 retrocopy	retro_pabe_427,
Pan troglodytes	ENSPTRG00000009220	2 retrocopies	retro_ptro_1624, retro_ptro_334,