RetrogeneDB ID: retro_nleu_1237

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397286.1:3304444..3305076(+)
• Located in intron of: ENSNLEG00000013865

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSNLEG00000012846
• Aliases: None
• Description: None

Sequence

>retro_nleu_1237
GCCGTGGCCCACTAGCGGGGTCTGGAGGACGGAGAAGAGGAGGAAGAGGAGGAGCAGTTGGTTCTAGTGGAATTATCAGG
AATTATTGATTCAGACTTTCTCTCAAATGTGAAAATAAATGCAAGGTTTTGGGCACTGACACTGAGAGGCCCATTCTGCA
AATGGGCACAGCTGTGTCTTTGCTGGGGAGTATGAAGACACTCTTGGGACCTGTGTTATATTTGAAGAAAATGTTTACCA
TGCTGATACACAAGGCAATAATAAAACAGTGCTAAAATATAAATGTCATACAATGAAGAAGCTCAGCATGACAAGAACTC
TTCTGACAGAGAAGAAGGAAGGAGAAGAAAACATAGGTGGGATGGAATGGTTGCAAATAAAGGATAATGATTTCTCCTAT
CGACCCAACATGATTTGTAGCTTTCTACATGAAAATGAAGACGAAGAAGTGGTAGCTTCAGCCCCAGAAATATCTTTGGA
ATTGGAAGAGGAAAAGATTCAAATGAACGAGAGTTCAAACCTGAGTTGTGAACAGGAGAAACCAATGCACTTGGAAATAG
AAGATTCTGGTCCTCTTATTGATATACCTTCTGAGAAAGAAAGTTGTTTTTATGGAAACTCAAATGCCGCCT

Alignment

ORF - retro_nleu_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.4 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAADERGPEDGEEEEEEEQLVLVELSGIIDSDFLS-KCENKCKVLGIDTERPILQVDSCV-FAGEYEDTL
          A.A..RG.EDG.......QLVLVELSGIIDSDFLS.KCENKCKVLG.DTERPILQ....V...G.....L
Retrocopy AVAH*RGLEDGXXXXXXXQLVLVELSGIIDSDFLS<KCENKCKVLGTDTERPILQMGTAVSLLGSMKTLL

Parental  G-TCVIFEENVEHADTEGNNRTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGGVEWLQIKDNDFSYRPNM
          G.TCVIFEENV.HADT.GNN.TVLKYKCHTMKKLSMTRTLLTEKKEGEENIGG.EWLQIKDNDFSYRPNM
Retrocopy G<TCVIFEENVYHADTQGNNKTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGGMEWLQIKDNDFSYRPNM

Parental  ICNFLHENEDEEVVASAPDKSLELEEEEIQMNDSSNLSCEQEKPMHLEIEDSGPLIDIPSETEGSVF-ME
          IC.FLHENEDEEVVASAP..SLELEEE.IQMN.SSNLSCEQEKPMHLEIEDSGPLIDIPSE.E.S.F.ME
Retrocopy ICSFLHENEDEEVVASAPEISLELEEEKIQMNESSNLSCEQEKPMHLEIEDSGPLIDIPSEKE-SCF>ME

Parental  TQMLP
          TQM.P
Retrocopy TQMPP

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_1237 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 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237 , retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,