RetrogeneDB ID: retro_nleu_2178

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:1266242..1266991(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LANCL3
• Ensembl ID: ENSNLEG00000000916
• Aliases: None
• Description: None

Sequence

>retro_nleu_2178
ATGGATACCAAGCGCTACTTCACCAATCGCTTCGATGACTACCAGGGCAGCCTGCTGGCGGGCCAGTGTGAGGAGGCGGT
GGCGTCCTTGGTCACCGCCACCATCCAGCGCATCCTGCAGGAGCTTCCCCCACTCGGGGCGGCGCCGAGGCCTGAGGGGC
GACGGTCAGGGCTAGCGGCTGCCGGGGGGGCTTTATGGCGGCGTGGCCAGAGTGGCCTACATCTACCACGTCTCGCAAAG
CCCGCTTTTCGCCAAGGCCCGGGAACGCTACCTGCGCTCAGCTATGCGCCTCATGGACGCGTGCGCCCGCGCTGAGGAGT
GGAGGGAACCGGACGCCCACACCCGCGCTGCCTTCCTGCTCGGGGGCGCGGGCGTGTACGCCGTCGCCACGCTCGTATAC
CACGCCCTGGGCGGGTCCGACTACGTGCAGCCGCTGGGCAAGTTCCGGGCTCTGTGTGCCGTCTGCGCGCCGGTCTCCTT
CCTGGAGTGCGGCTCCGACGAGCCGTCCGTGGGCCGCGCGGGCTACCTGTGTGCGGCGCTGGTGCTCAAGCAGAAAACTC
GCCCAGGAGGTAAGAGGTAGTCCCGGCCGCGGGAGGGCGCTCGCCGCCTGCCCAGCCTCCCTTCGGGACTCGGTGGCTAG
GGCAGCACTGCCCCGGGTTGCTCTCCATGTCTGTTACTCTTGGTGTGGTGCTAGCATTTCTTCAGTCTCTTGAGGTTTAT
CTCCTGCTTTTGTCCGTCTTCTTTCCTTT

Alignment

ORF - retro_nleu_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.02 %
• Parental protein coverage: 59.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDTKRCFANRFDDYQGSLLAGQCEEAVAPLVTATIERILQELPPLG-GGAEARGATAGASGCQGG-LYGG
          MDTKR.F.NRFDDYQGSLLAGQCEEAVA.LVTATI.RILQELPPLG.GGAEA.GAT..ASGC.GG.LYGG
Retrocopy MDTKRYFTNRFDDYQGSLLAGQCEEAVASLVTATIQRILQELPPLG<GGAEA*GATVRASGCRGG<LYGG

Parental  VAGVAYMLYHVSQSPLFATARERYLRSAKRLIDACARAEEWGEPDADTRAAFLLGGAGVYAVATLVYHAL
          VA.VAY..YHVSQSPLFA.ARERYLRSA.RL.DACARAEEW.EPDA.TRAAFLLGGAGVYAVATLVYHAL
Retrocopy VARVAY-IYHVSQSPLFAKARERYLRSAMRLMDACARAEEWREPDAHTRAAFLLGGAGVYAVATLVYHAL

Parental  GRSDYVQPLGKFRALCAVCAPVSFLECGSDELFVGRAGYLCAALVLKQ-KLAQEVL-TPAQIKSI--CQA
          G.SDYVQPLGKFRALCAVCAPVSFLECGSDE..VGRAGYLCAALVLKQ.KLAQEV...P........C.A
Retrocopy GGSDYVQPLGKFRALCAVCAPVSFLECGSDEPSVGRAGYLCAALVLKQ>KLAQEVRGSPGRGRALAACPA

Parental  ILDSGKQYAIKKRKPFPLMYSYYGTEYLGAAHGLSSILQMLLSY
          .L......A...R......YS..G........GLS.....LLS.
Retrocopy SLRDSVARAALPRVALHVCYSWCGASISSVS*GLSPAFVRLLSF

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_2178 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014625	1 retrocopy	retro_meug_1916,
Nomascus leucogenys	ENSNLEG00000000916	1 retrocopy	retro_nleu_2178 ,
Pan troglodytes	ENSPTRG00000021790	1 retrocopy	retro_ptro_3193,