RetrogeneDB ID: retro_nleu_2867

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397457.1:383445..384226(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAPCD2
• Ensembl ID: ENSNLEG00000008908
• Aliases: None
• Description: None

Sequence

>retro_nleu_2867
ATGGCCCGGGCCGCGACAGCGGAGCAGGGCCGCGTGCCTCCCGCCGCGCCTGCGCGCAGCAGGGAGGGGCTGCTGCGCGG
CTTCCTGCAGAGCCTGCCCACCCTGTTCGACATTCTGGACGACCGACGGCGCCGCTGCTGCACCTGCGCGAGATCTAGTC
CCGCTGGCAGGGCGCCGACGCGCGGGAGCTGTCCAGCGTGGTGCTGGAGGGCTTGCGCCAGATGGCCCCGGCCAGTGGCT
GCCTGACTTTCGAGCGCTTGCTGACCGGCCTGCGCACCTCTCTGCTGAGCGCCGACGGCGGCCCCCGGAACCCCATGCGT
GCCCCGGCCGGCCCGGGGACCAGCCGCCGCCGCAGGGCCTGGTATTCGCGCGGGCCGACGAGCCGCGGACGGTCCTGGAG
AGGAAGCCCCTGCCCCTGGGCGTGCGCGCCCCTTTGGCCGGTCCCAGCTGCGCGGCCGCAGCAGGAGCAGTTGTGCGCCC
CTGCCAAGGCGGCGTCCTGCCCCGCGGAGCCCGAGCTGTCCCAGAGTGCGGCGCTGGAACGGAGCTTGAGCGCCGACGCA
GGTGCAGCGGCCTGCAGGGTCCTGGAGGCGGACTCAGGGGATGCCCGTCGGGCCCCGCTTGCCGGAGGGGAACACGGGAG
GCACATCATCACCAGCGGCTGGACTGCGGCCTGCTGAAGCAGATGAAGGAGCTGGAGCAGGAGGAGGATGTGCTGCTGCA
GGGTTTGGAGATAATGGCGCGGGGCCGCGATTGGTACCAGCAGCAGCTGCAACGAGTGCAG

Alignment

ORF - retro_nleu_2867 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 67.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAGAAMAERGRVPPPAPAPSTEGLPRAFLQSLRTLFDILDDRRRGC-VHLREIESRWQGTDARELPRGVL
          MA.AA.AE.GRVPP.APA.S.EGL.R.FLQSL.TLFDILDDRRR.C..HLREI.SRWQG.DAREL...VL
Retrocopy MARAATAEQGRVPPAAPARSREGLLRGFLQSLPTLFDILDDRRRRC<LHLREI*SRWQGADARELSSVVL

Parental  EGLRQVAPASGYLTFERFVAGLRTSLLSADGGPRDPTRAPA-RPGDQPPLPPQRLVFAPADEPRTVLERK
          EGLRQ.APASG.LTFER...GLRTSLLSADGGPR.P.RAPA.RPGDQPP..PQ.LVFA.ADEPRTVLERK
Retrocopy EGLRQMAPASGCLTFERLLTGLRTSLLSADGGPRNPMRAPA<RPGDQPP--PQGLVFARADEPRTVLERK

Parental  PLPLGVRA-PLADSSPAFRSTHSA-CAPACPPAAPASPRRLQRVAGEPGPCLSTTGAVACRALEADSADA
          PLPLGVRA.P...S....RS..S..CAPA.....PA.P...Q..A.E........GA.ACR.LEADS.DA
Retrocopy PLPLGVRA<PFGRSQLRGRSRSSC<CAPAKAASCPAEPELSQSAALERS-LSADAGAAACRVLEADSGDA

Parental  RRAPRARGERRRHTITSG-VDCGLLKQMKELEQEKEVLLQGLEMMARGRDWYQQQLQRVQ
          RRAP.A.GE..RH.ITSG..DCGLLKQMKELEQE..VLLQGLE.MARGRDWYQQQLQRVQ
Retrocopy RRAPLAGGEHGRHIITSG<LDCGLLKQMKELEQEEDVLLQGLEIMARGRDWYQQQLQRVQ

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_2867 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734, retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867 , retro_nleu_2939,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222, retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530, retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,