RetrogeneDB ID: retro_nleu_128

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01135303.1:19971..21243(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000013197
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MBTD1
• Ensembl ID: ENSNLEG00000007934
• Aliases: None
• Description: None

Sequence

>retro_nleu_128
ATGTTTGACGGTTATGATAGCTGCAGTGAGGACACAAGCAGCAGCTCCAGCTCCGAAGAGAGTGAGGAAGAAGTCTCTCC
TTTACCTTCTAATCTCCCGATTATCAAAAACAATGGGCAAGTCTACACATACCCAGATGGTAAATCTGGCATGGCTACCT
GCGAGATGTGTGGGATGGTTGGCGTCCGAGATGCTTTTTACTCTAAAACAAAGCGTTTCTGTAGCGTTTCATGTTCAAGA
AGTTACTCGTCAAACTCCAAGAAGGCAAGCATTTTGGCCAGACTTCAGGTAACGGGTAAGCCTCCAACAAAGAAAGCAAA
AGTTCTTCAGAAACAACCTTTAGTTGCTAAGCTAGCCGCATATGCTCAATATCAAGCTACCTTGCAAAATCAAGCAAAGA
CAAAAGCAGCAGTCTCCATGGAAGGTTTCAGCTGGGGTAACTACATCAATAGCAATAGCTTTATAGCAGCTCCGGTTACC
TGTTTTAAACATGCACCTATGGGGACCTGCTGGGGTGATATCTCAGAAAATGTGAGAGTAGAAGTTCCCAATACAGACTG
CAGCCTACCTACCAAAGTCTTCTGGATTGCTGGAATAGTAAAATTAGCAGGTTACAATGCCCTTTTAAGATATGAAGGAT
TTGAAAATGACTCTGGTCTGGACTTCTGGTGCAATATATGTGGTTCTGATATCCATCCAGTTAGTTGGTGTGCAGCCAGC
GGAAAACCTCTTGTTCCTCCTAGAACTATTCAGCATAAATACACAAACTGGAAAGCTTTTCTAGTGAAATGACTTACTGG
TGCCAAAACACTGCCTCCTGATTTCTCACAAAAGGTTTCAGAGAGTATGCAGTATCCTTTCAAACCTTGCATGAGAGTAG
AAGTGGTTGACAAGAGGCATTTGTGTCGAACACGAGTAGCAGTGGTGGAAAGTGTAATTGGAGGAAGATTAAGACTAGTG
TATGAAGAAAGCGAAGATAGAACAGATGACTTCTGGTGCCATATGCACAGCCCATTAATACATCATATTGGTTGGTCTCA
AAGCATAGGTCATCGATTCAAAAGATCTGATATTACAAAGAAACAAGATGGACATTTTGATACACCACCACATTTATTTG
CTAAGGTAAAAGAAGTAGACCAGAGTGGGGAATGGTTCAAGGAAGGAATGAAATTGGAAGCTATAGACCCATTAAATCTT
TCTACAATATGTGTCACAACCATTAGAAAGGTGCTAGCTGACGGATTCCTGATGATTGGGATCGATGGCTCA

Alignment

ORF - retro_nleu_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.99 %
• Parental protein coverage: 97.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFDGYDSCSEDTSSSSSSEESEEEVAPLPSNLPIIKNNGQVYTYPDGKSGMATCEMCGMVGVRDAFYSKT
          MFDGYDSCSEDTSSSSSSEESEEEV.PLPSNLPIIKNNGQVYTYPDGKSGMATCEMCGMVGVRDAFYSKT
Retrocopy MFDGYDSCSEDTSSSSSSEESEEEVSPLPSNLPIIKNNGQVYTYPDGKSGMATCEMCGMVGVRDAFYSKT

Parental  KRFCSVSCSRSYSSNSKKASILARLQ--GKPPTKKAKVLQKQPLVAKLAAYAQYQATLQNQAKTKAAVSM
          KRFCSVSCSRSYSSNSKKASILARLQ..GKPPTKKAKVLQKQPLVAKLAAYAQYQATLQNQAKTKAAVSM
Retrocopy KRFCSVSCSRSYSSNSKKASILARLQVTGKPPTKKAKVLQKQPLVAKLAAYAQYQATLQNQAKTKAAVSM

Parental  EGFSWGNYINSNSFIAAPVACFKHAPMGTCWGDISENVRVEVPNTDCSLPTKVFWIAGIVKLAGYNALLR
          EGFSWGNYINSNSFIAAPV.CFKHAPMGTCWGDISENVRVEVPNTDCSLPTKVFWIAGIVKLAGYNALLR
Retrocopy EGFSWGNYINSNSFIAAPVTCFKHAPMGTCWGDISENVRVEVPNTDCSLPTKVFWIAGIVKLAGYNALLR

Parental  YEGFENDSGLDFWCNICGSDIHPVGWCAASGKPLVPPRTIQHKYTNWKAFLVKRLTGAKTLPPDFSQKVS
          YEGFENDSGLDFWCNICGSDIHPV.WCAASGKPLVPPRTIQHKYTNWKAFLVK.LTGAKTLPPDFSQKVS
Retrocopy YEGFENDSGLDFWCNICGSDIHPVSWCAASGKPLVPPRTIQHKYTNWKAFLVK*LTGAKTLPPDFSQKVS

Parental  ESMQYPFKPCMRVEVVDKRHLCRTRVAVVESVIGGRLRLVYEESEDRTDDFWCHMHSPLIHHIGWSRSIG
          ESMQYPFKPCMRVEVVDKRHLCRTRVAVVESVIGGRLRLVYEESEDRTDDFWCHMHSPLIHHIGWS.SIG
Retrocopy ESMQYPFKPCMRVEVVDKRHLCRTRVAVVESVIGGRLRLVYEESEDRTDDFWCHMHSPLIHHIGWSQSIG

Parental  HRFKRSDITKKQDGHFDTPPHLFAKVKEVDQSGEWFKEGMKLEAIDPLNLSTICVATIRKV-TQNFLLNG
          HRFKRSDITKKQDGHFDTPPHLFAKVKEVDQSGEWFKEGMKLEAIDPLNLSTICV.TIRKV....FL..G
Retrocopy HRFKRSDITKKQDGHFDTPPHLFAKVKEVDQSGEWFKEGMKLEAIDPLNLSTICVTTIRKVLADGFLMIG

Parental  LTTS
          ...S
Retrocopy IDGS

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_128 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007934	1 retrocopy	retro_nleu_128 ,
Pongo abelii	ENSPPYG00000008267	1 retrocopy	retro_pabe_2472,