RetrogeneDB ID: retro_nleu_2700

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397401.1:3950697..3951361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GXYLT1
• Ensembl ID: ENSNLEG00000017947
• Aliases: None
• Description: glucoside xylosyltransferase 1 [Source:HGNC Symbol;Acc:27482]

Sequence

>retro_nleu_2700
ACACTGATAGCCTTTTTACGACCTGTTGATCATATTTGTTCTTTACTAAAGAAATTTAATTCCACATAAATTGCTGCAGT
GGCCTCAGCACACAAGGTACCTCAAATAAAATGGTATAGTCGCTTTGTTAGGCAACCATACTGTGCAAAAACTGGAGTAA
ACCCTGGAGTTATGTTGATGAATATGACTCGAATGAGAAGGAAGTATTTCAAGAATGATATGACAACTGTGTGACTACAG
TGAGGAGATATACTTATGACATGGCTTAAAGAATACAAACTAAGCATTACATGGGCGATCAAGATCTGTTGGATATCATG
TTTTTTCCTAATCCAGAAAGTCTTTTCGCCTTTTCATGTCAATGGAATTATCATCCAGTTCATTGTCTACATGGAAGCAG
TTGCCAAGAAGCAGAAGAAGGAATCTTTATTCTTCATGGGAGCAGAGGTGTTTACCATGATGATAAGCAACCAGCATTTA
GAGCTGTTTATGAAGCACTAAGAAATTGTTCTTTTAAGATGACAACATTCATTCCCTAATAAAACCTTTAGAACTGGAAC
TACAAAAAACAGTGCATACATACCTTGGAAAAATTTACAAAATATTTATCAAACAACTAGCAAAAAGCATAAGAGATCGT
TATGCCAGATCACCAAAGGAAAGG

Alignment

ORF - retro_nleu_2700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.44 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDILFLRPIDDIWSLLKKFNSTQIAAMAPEHEEPRIGWYNRFARHPYYGKTGVNSGVMLMNMTRMRRKYF
          T.I.FLRP.D.I.SLLKKFNST.IAA.A..H..P.I.WY.RF.R.PY..KTGVN.GVMLMNMTRMRRKYF
Retrocopy TLIAFLRPVDHICSLLKKFNST*IAAVASAHKVPQIKWYSRFVRQPYCAKTGVNPGVMLMNMTRMRRKYF

Parental  KNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIMFFHNPESLFVFPCQWNYRPDHCIYGSNCQEAE
          KNDMTTV.LQ.GDILM..LK.YKL.ITW.GDQDLL.IMFF.NPESLF.F.CQWNY.P.HC..GS.CQEA.
Retrocopy KNDMTTV*LQ*GDILMTWLKEYKLSITW<GDQDLLDIMFFPNPESLFAFSCQWNYHPVHCLHGSSCQEA-

Parental  EEGIFILHGNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRSLLKPLELELQKTVHTYCGKIYKIFIKQL
          EEGIFILHG.RGVYHDDKQPAFRAVYEALRNCSF..DDNI.SL.KPLELELQKTVHTY.GKIYKIFIKQL
Retrocopy EEGIFILHGSRGVYHDDKQPAFRAVYEALRNCSFK<DDNIHSLIKPLELELQKTVHTYLGKIYKIFIKQL

Parental  AKSVRDRYARSPKEK
          AKS.RDRYARSPKE.
Retrocopy AKSIRDRYARSPKER

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_2700 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700 ,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849, retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754,