RetrogeneDB ID: retro_nleu_2994

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397557.1:25558..26388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THAP5
• Ensembl ID: ENSNLEG00000008290
• Aliases: None
• Description: None

Sequence

>retro_nleu_2994
ATGCCCCACTATTGCACAGCGATTTGTTGTAAGAACCGCCGGGGACGAAACAATAAAGACCGGAAGCTGAGTTTTTATCC
ATTTCCTCTTCATGACAAAGAAAGACTGGAGAAGTGGTTAAAGAATATGAAGCAAGATTCACGGGTTCCCAGTAAATACC
AGTTTCTATGTAGTGACCATTTTACTCCTGACTCTCTTGACATCAGATGGGGTATTCGATATTTAAAACAAACTGCAGTT
CCAACAATATTTTCTTTGCCTGAAGACAATCAGAGAAAAGACCCTTCTAAAAAAAAATCCCAGAAGAAAAACTTGGAAGA
TGAGAAAGAAGTATGCCCAAAGGCCAAGTCAGAAGAATCAGTTGTATTAAATGAGACAAAGAAAAATATAGTTAACACAA
ATGTGCCCCCTCAACATCCAGAATTACTTACTTCATTCATCTTCTTTGGTTAAGCCACCAGCTCCTAAAACAGGAAGTAT
ACAAAATTACATGTTAACTCTTAATCTAGTTAAACAACATACTGGGAAACCAGAATCTACCTTGGAAACATCAGTTAACC
AAGATACAGGTATAGATGGTTTTCACACGTTTTGAGAATCTAAATTCTACAACTATTACTTTGACAACTTCAAATTCAGA
AAGTATTCATCAATCTTTGGAAACCCAAGAAGTTCTTGAAGTAACTTCTAGTCATCTTGCTAATCCAAACTTTACAAGTA
ATTCCATGGAAATAAAGTCAGCACAGGAAAATCCATTCTTATTCAGCACAATTAATCAAACAGTTGAATTAAACACAAAG
AATCTGTTATTGCCATTTTTGTACCTGCCG

Alignment

ORF - retro_nleu_2994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.93 %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPRYCAAICCKNRRGRNNKDRKLSFYPFPLHDKERLEKWLKNMKRDSWVPSKYQFLCSDHFTPDSLDIRW
          MP.YC.AICCKNRRGRNNKDRKLSFYPFPLHDKERLEKWLKNMK.DS.VPSKYQFLCSDHFTPDSLDIRW
Retrocopy MPHYCTAICCKNRRGRNNKDRKLSFYPFPLHDKERLEKWLKNMKQDSRVPSKYQFLCSDHFTPDSLDIRW

Parental  GIRYLKQTAVPTIFSLPEDNQGKDPSKNKSQKKNLEDEKEVCPKAKSEESFVLNETKKNIVNTNVPPQHP
          GIRYLKQTAVPTIFSLPEDNQ.KDPS...SQKKNLEDEKEVCPKAKSEES.VLNETKKNIVNTNVPPQHP
Retrocopy GIRYLKQTAVPTIFSLPEDNQRKDPSXXXSQKKNLEDEKEVCPKAKSEESVVLNETKKNIVNTNVPPQHP

Parental  ELLHS-SS-LVKPPAPKTGSIQNNMLTLNQVKQHTGKPESTLETSVNQDTGIGGFHTRFENL-NSTTITL
          ELL.S.SS.LVKPPAPKTGSIQN.MLTLN.VKQHTGKPESTLETSVNQDTGI.GFHT..E.....T....
Retrocopy ELLTS>SSSLVKPPAPKTGSIQNYMLTLNLVKQHTGKPESTLETSVNQDTGIDGFHTF*ESK>STTITLT

Parental  TTSNSESIHQSLETQEALEVTTSHHANPNFTSNTMEIKSAQENPFLFSTINQTVEELNTNKESVIAIFVP
          T....ESIHQSLETQE.LEVT.SH.ANPNFTSN.MEIKSAQENPFLFSTINQTV.ELNT..........P
Retrocopy TSNS-ESIHQSLETQEVLEVTSSHLANPNFTSNSMEIKSAQENPFLFSTINQTV-ELNTKNLLLPFLYLP

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_2994 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003290	1 retrocopy	retro_cfam_1931,
Homo sapiens	ENSG00000177683	1 retrocopy	retro_hsap_3924,
Myotis lucifugus	ENSMLUG00000015130	1 retrocopy	retro_mluc_1285,
Nomascus leucogenys	ENSNLEG00000008290	1 retrocopy	retro_nleu_2994 ,
Nomascus leucogenys	ENSNLEG00000008620	1 retrocopy	retro_nleu_1846,