RetrogeneDB ID: retro_nleu_2158

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397332.1:10082568..10083801(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRADB
• Ensembl ID: ENSNLEG00000006967
• Aliases: None
• Description: None

Sequence

>retro_nleu_2158
AGTTCAAGAACACAAGTTGAATCACTCAAACATGAAAAACAAGTCTGAAACCAGTATCCATCAATACTTGGTCGATGAGG
CAATCCTTTCCTGGTCGCCTCCATCCACTAGAGCCAGCGAAGTAGTATGTTCCACCAACGTTTCTCACTATGAGCTCCAA
GGAGAAATAGGAAGAGGATTTGACAACTTGACTTCTGTCCATCTCGCACGGCATACTCCTACGGGAACACTGGTAACTAT
AAAAACTACAAATCTGGAAAACTGCAATGAAGGACGCCTGAAAGTTTTACGGAAAGCCATGATTCTATCCCACTTTTTCC
GGCATCCCAATATTACAACTTCTTGGACAGTTTTCACTGTTGGCAGCTGGCTTTGGGTTATTTCTCCATTTATGGCCTAT
GGTTCAGCAAGTCAACTCTTGAGGACCTATTTTCCTGAAGGAATGAGTAAAACTTTAATAAGAAACATTCTCTTTGGAGC
AGTGAGAGGATTGAACTATCTCTACCAATATGGCTGTATTCACAGGAGTATTAAAGCCAGCCGTATCCTCATTTCTGGTG
ATGGCCTAGTGACCCTCTCTGGCCTGTCCCATCTGCATAGTTTGGTTAAGCATGGACAGAAGCATAGGGCTGTGTACGAT
TTCCCACAGTCCAGCACATCAGTGCATCCATGGCTGAGTCCAGAACTACTGAGATAGGATTTACATGGGTATAATGTGAA
GTCAGATATTTACAGTGTTGGGATTGCAACATGTGAATTAGCCAGTGGGCAGGTGCCTTTCCAGGACATGCATAGAACTC
AGATGCTGTTAACGGAAACTGAAAGGTCCCCCTTATAGCCCATTGGATATCAGTATTTTCCCTCAATCAGAATCCAAAAT
GAAAAATTCCCGGTCAGGTGTAGACTCTGGGATTGGAGCAAGTGTGCTTGTCTCCAGTGGAACTCACACAGTAAATAGTG
ACCGATTACACACACCATCCTCAAAAACCTTCTCTCCTGCCTTCTTTAGCTTGGTACAGCTCTGTTTGCAATAAGATCCG
GAGAAAAGGCCATCAGCAAGCAGTTTATTGTCCCATGTTTTCTTCAAACAGATGAAAGAAGAAAGCCAGGATTCAATACT
TTCACTGTTGCCTCCTGCTTATAACAAGCCATCAATATCACTGCCTCCGGTGTTACCTTGGACTGAGCCAGAATGTGATT
TTCCTGATGAAAAAAGACTCATATGGGGAATTC

Alignment

ORF - retro_nleu_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 98.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSRTQVESLRPEKQ-SETSIHQYLVNEPTLSWSPPSTRASEVLCSTNVSHYELQVEIGRGFDNLTSVHLA
          .SRTQVESL..EKQ.SETSIHQYLV.E..LSWSPPSTRASEV.CSTNVSHYELQ.EIGRGFDNLTSVHLA
Retrocopy SSRTQVESLKHEKQ>SETSIHQYLVDEAILSWSPPSTRASEVVCSTNVSHYELQGEIGRGFDNLTSVHLA

Parental  RHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMAYGSASQL
          RHTPTGTLVTIK.TNLENCNE.RLK.L.KA.ILSHFFRHPNITT.WTVFTVGSWLWVISPFMAYGSASQL
Retrocopy RHTPTGTLVTIKTTNLENCNEGRLKVLRKAMILSHFFRHPNITTSWTVFTVGSWLWVISPFMAYGSASQL

Parental  LRTYFPEGMSETLIRNILFGAVRGLNYTHPKWRIHRSIKASHILISGDGLVTLSGLSHLHSLVKHGQRHR
          LRTYFPEGMS.TLIRNILFGAVRGLNY......IHRSIKAS.ILISGDGLVTLSGLSHLHSLVKHGQ.HR
Retrocopy LRTYFPEGMSKTLIRNILFGAVRGLNYLYQYGCIHRSIKASRILISGDGLVTLSGLSHLHSLVKHGQKHR

Parental  AVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLL-QKLKGPPY
          AVYDFPQ.STSV.PWLSPELLR.DLHGYNVKSDIYSVGI..CELASGQVPFQDMHRTQMLL..KLKGPPY
Retrocopy AVYDFPQSSTSVHPWLSPELLR*DLHGYNVKSDIYSVGIATCELASGQVPFQDMHRTQMLL>RKLKGPPY

Parental  SPLDISIFPQSESRMKNSRSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCLQQDPEK
          SPLDISIFPQSES.MKNSRSGVDSGIG.SVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCLQ.DPEK
Retrocopy SPLDISIFPQSESKMKNSRSGVDSGIGASVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCLQ*DPEK

Parental  RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDE-KDSYWEF
          RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDE.KDSY.EF
Retrocopy RPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDE>KDSYGEF

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_2158 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000082146	2 retrocopies	retro_hsap_147, retro_hsap_3920,
Gorilla gorilla	ENSGGOG00000012183	1 retrocopy	retro_ggor_2638,
Macaca mulatta	ENSMMUG00000018141	1 retrocopy	retro_mmul_1741,
Nomascus leucogenys	ENSNLEG00000006967	1 retrocopy	retro_nleu_2158 ,
Otolemur garnettii	ENSOGAG00000010744	1 retrocopy	retro_ogar_1019,
Pongo abelii	ENSPPYG00000013074	1 retrocopy	retro_pabe_3192,