RetrogeneDB ID: retro_nleu_2778

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397427.1:2140758..2141498(+)
• Located in intron of: ENSNLEG00000011334

Retrocopy information

• Ensembl ID: ENSNLEG00000011350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSNLEG00000009532
• Aliases: None
• Description: None

Sequence

>retro_nleu_2778
CGCAGTAAGACCTATGGCAACGTGCTGGTGTTGGACGGTGTCATCCAGTGCACAGAGAGAGACGAGTTCTACGAGGAGAT
GATCGCCAACCTGCCTCACTGCAGCCACTCCAACCCGCGAAGGGTGCTGATCATCGGGGGCCGAGATAGAGGTGTCCTGC
GTGAGGTGGTGAAGCATCCCTCCGTGGAGTCCGTGGTCCAGTGTGAGATCGACGAGGATGTCATCCAAGTCTCCAAGAAG
TTCCTGCCAGGCATGGCCTTTGGCTACTCTAGCTCGAAGCTGACCCTACATGTGGGTGACGATTTTGAGTTCATGAAACA
GAATCAGGATGCCTTCGATGTGATCATCACTGACTCCTCAGACCCCATGGGCCCCGCCGAAACTCTCTTCAAGGAGTCCT
ATTACCAGCTCATGAAGACAGCCCTCAAGGAAGATGGTGTCCTCTGCTGCCAGGGCGAGTGCCAGTGGCTGCACCTGGAC
CTCATCAAGGAGATGCAGCAGTTCTGCCAGTCCTTGTTCCCCATGGTGGCCTACGCCTACTGCACCATCCCCACCTACCC
CAGCGGCCAGATCGGCTTCATGCCCTGCAGCAAAAACCCAAGCACCAACTTCAGGAGCCGGTGTAGCCGCTGATGCAGCA
GCAGGTGGCGCAGATGCAACTGAAGTACTACAACTCCGATGTGCACCGCGCTGCCTTGGTGCTGCCCGAGTTTGCCCGCA
AGGCCCTGAATGATGTGAGC

Alignment

ORF - retro_nleu_2778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCE
          RSKTYGNVLVLDGVIQCTERDEF.Y.EMIANLP.CSH.NPR.VLIIGG.D.GVLREVVKHPSVESVVQCE
Retrocopy RSKTYGNVLVLDGVIQCTERDEF-YEEMIANLPHCSHSNPRRVLIIGGRDRGVLREVVKHPSVESVVQCE

Parental  IDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMK
          IDEDVIQVSKKFLPGMA.GYSSSKLTLHVGD.FEFMKQNQDAFDVIITDSSDPMGPAE.LFKESYYQLMK
Retrocopy IDEDVIQVSKKFLPGMAFGYSSSKLTLHVGDDFEFMKQNQDAFDVIITDSSDPMGPAETLFKESYYQLMK

Parental  TALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNF-QEPV
          TALKEDGVLCCQGECQWLHLDLIKEM.QFCQSLFP.VAYAYCTIPTYPSGQIGFM.CSKNPSTNF.QEPV
Retrocopy TALKEDGVLCCQGECQWLHLDLIKEMQQFCQSLFPMVAYAYCTIPTYPSGQIGFMPCSKNPSTNF<QEPV

Parental  QPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALNDVS
          .PL.QQQVAQMQLKYYNSDVHRAA.VLPEFARKALNDVS
Retrocopy *PLMQQQVAQMQLKYYNSDVHRAALVLPEFARKALNDVS

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_2778 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778 ,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975,