RetrogeneDB ID: retro_nleu_2191

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:9697621..9698166(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLLP
• Ensembl ID: ENSNLEG00000002825
• Aliases: None
• Description: None

Sequence

>retro_nleu_2191
ATGGCCGAGTTCCCGTCAAAAGCGAGCACGCGGACCAGCAGTACCGCGCAGGACGCCGTAGCCTTGGTGTAGGCGCTGCG
CACGGACCTGGGCTTCGTGCGCTCCCGCCTCGGGACGTTCATGCTGCTGCAGCTGGTGCTGGGGCTGCTGGTGTGGGCCC
TGATTGCGGACACCCTGTACCACCTGTACCTGGCCTATGGCTGGGTGATGTTCGTAGCTGTCTTCCTCTGGCTGGTGACA
ATCGTCTTCTTCCCCCTCTACCTGTTTCAGCTGCACATGAAGTTGTACATGGTGCCCTGGCCACTAGTGTTAATGATGTT
TAACGTCAGTGCCACCGTTCTGTACGTCACCGCCTTCATCGCCTGCTCTGCGGCAGTTGACCTGACGTCCCTGAAGGGCA
CGCAGCCGTATAACCAGCGTGCGGCTACCTCGTTCTTTGCGTGTTTGGTGATGATCGCCTACGGAGTGAGCACCTTCTTC
AGCTACCATGCCTGGCGAGGAGTAGGCAGCAATGCACCACCAGTCAGATGGCTGGCGGCTATGCC

Alignment

ORF - retro_nleu_2191 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEFPSKVSTRTSSPAQGAGASVSALRPDLGFVRSRLGALMLLQLVLGLLVWALIADTPYHLYPAYGWVM
          MAEFPSK.STRTSS.AQ.A.A.V.ALR.DLGFVRSRLG..MLLQLVLGLLVWALIADT.YHLY.AYGWVM
Retrocopy MAEFPSKASTRTSSTAQDAVALV*ALRTDLGFVRSRLGTFMLLQLVLGLLVWALIADTLYHLYLAYGWVM

Parental  FVAVFLWLVTIVLFILYLFQLHMKLYMVPWPLVLMIFNISATVLYITAFIACSAAVDLTSLRGTRPYNQR
          FVAVFLWLVTIV.F.LYLFQLHMKLYMVPWPLVLM.FN.SATVLY.TAFIACSAAVDLTSL.GT.PYNQR
Retrocopy FVAVFLWLVTIVFFPLYLFQLHMKLYMVPWPLVLMMFNVSATVLYVTAFIACSAAVDLTSLKGTQPYNQR

Parental  AAASFFACLVMIAYGVSAFFSYQAWRGVGSNA-ATSQMAGGYA
          AA.SFFACLVMIAYGVS.FFSY.AWRGVGSNA..TSQMAGGYA
Retrocopy AATSFFACLVMIAYGVSTFFSYHAWRGVGSNA<TTSQMAGGYA

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_2191 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012103	1 retrocopy	retro_cjac_4155,
Homo sapiens	ENSG00000102934	1 retrocopy	retro_hsap_4816,
Loxodonta africana	ENSLAFG00000008636	1 retrocopy	retro_lafr_145,
Macaca mulatta	ENSMMUG00000008924	1 retrocopy	retro_mmul_2569,
Nomascus leucogenys	ENSNLEG00000002825	1 retrocopy	retro_nleu_2191 ,
Oryctolagus cuniculus	ENSOCUG00000007353	1 retrocopy	retro_ocun_685,
Pongo abelii	ENSPPYG00000007385	1 retrocopy	retro_pabe_3744,
Pan troglodytes	ENSPTRG00000008151	1 retrocopy	retro_ptro_3205,