RetrogeneDB ID: retro_nleu_3085

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397897.1:40292..41820(-)
• Located in intron of: ENSNLEG00000010480

Retrocopy information

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

Parental gene information

• Parental gene symbol: FLYWCH1
• Ensembl ID: ENSNLEG00000009480
• Aliases: None
• Description: None

Sequence

>retro_nleu_3085
ATGCCCCTGCCCGAGCCCAGCGAGCAGGAGGGCGAAGAGTGTGAAGGCCAGCCGGGAGCCATCCCCCGAGCCAGCCACGG
ACGTTGTCCGGGCAGCCCCCAGGAAGCCCCAGGGAGTTCTCCAAACTGGTCCTGCTCACAGACTCCAACCAAGATGAGGA
AACGGTGGGATCCAAGCCCCAGGAAGTGCACTGCGTCCTGTCCCTGGAGATGGCTGGCCCCGCCACCCTCGTCAGCACCT
TGCAGATCCTGCCAGTTGAGCAGGGAGGGGTGGTCCAGCCAGCCCCACAGATGCCTGAACAGAAGTGCAGCAAGCTGGAC
ACAGCAGCCCCTCAGTCCCTGGAGTTCCTGAGGACACCATTCGGGGGCCACCTCCTGGTGCTGGAGTCCTTCCTGTACAA
GCAGGAGAAGGCTGTGGGGGACAAGGTATACTGGAGTGCCGCCAGCATGCTGAGCTGGGCTGCCCGGGCCGGGCCATCAC
CCGAGGCCTGCGGGCCACAGTGATGCGGGGCCACTGCCACGCGCCCAATGAGCAAGGCATGGAGGCCTGGCGCCAGAGGG
AGAAGCTGCCCAGCCTGGCCCTGCCAGAGGGCTTGGGAGAGCCCCAGGGTCCTGAGGGCCCTGGAGGCCGAGTGGAGGAG
CCACTGGAGGGGGTGGGCCCGTGGCAGTGCCCTGAGGAGCCAGAGCCAGAGCCCACTCCTGGGCTGGTGCTGAGCAAGCC
AGCCCCGGAGGAAGAGGGACCCCGAGCCCTGTCACTGCTGAGCCTGCCGCCCAAGAAGCGCTCGATCCTGGGGCTGGGAC
AGGCCCGGCCCCTCGAGTTCCTGAGGACGTGCTACGGGGGCAGCTTCCTGGTACACGAGTCATTCCTCTGCAAGCGGGAG
AAGGCTGTCGGGGACAAGGTGTATTGGACCTGCCGGGACCACGCGCTGCACAGCTGCTGGAGCCGGGCCATCACCCGGGG
ACAGCGGGTGACCGTGATGCGTGGGCACTGCCACCAGCCCGATATGGAGGGCCTGGAAGCCCGGCGGCAGCAGGAGAAGG
CCATGGAGACGCTGCAGGCTGGGCAGGACGGCCCTGGGAGCCAAGTGGACACGCTGCTCCAAGGCGTGGATAGTCTGCTC
TACCGCAGGGGTCCGGGTCCCCTGACTCTCACCAGGCCTCGGCCCAGAAAGCGAGCAAAGGTTGAAGACCAGGAGCTGCC
AATCCAGCCCGAGGCCCCAGAAGGATCCCCAGACGAGGACCAGGACATGGACGCAGACCCTGGAGGCCGTGAGTTCCTGA
AGACGCCCCTGGGGAGCAGCTTCCTGGTGTACGAGTCCTTCCTCTACCGGCGGGAGAAGGCGGCCGGGGAGAAGGTGTAT
TGGACCTGCCGGGACCAGGCCCTCCGCATGGGCTGCCGCAGCCGCGCCATGACCCAGGGCCGGCGGGTCATGGTCATGCG
CAGGCACTGCCACCCACCAGACCTGGGCGGCCTGGAAGCCCTGCGGAAGCGGGAGCACTTCCCCAGCCTGGCGCAGTGGG
ACAGCCCA

Alignment

ORF - retro_nleu_3085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 91.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPLPEPSEQEGD-SVKAGQEPSPEPATDVVPAAPRKP-REFPKLVLLTASNQDEDGVGSKPQEVHCVLSL
          MPLPEPSEQEG..SVKA..EPSPEPATDVV.AAPRKP.REF.KLVLLT.SNQDE..VGSKPQEVHCVLSL
Retrocopy MPLPEPSEQEGE>SVKASREPSPEPATDVVRAAPRKP>REFSKLVLLTDSNQDEETVGSKPQEVHCVLSL

Parental  EMAGPATLASTLQILPVEEQGGVVQPALQMPEQKCSKLDTAAPRSLEFLRTPFGGRLLVLESFLYKQEKA
          EMAGPATL.STLQILPVE.QGGVVQPA.QMPEQKCSKLDTAAP.SLEFLRTPFGG.LLVLESFLYKQEKA
Retrocopy EMAGPATLVSTLQILPVE-QGGVVQPAPQMPEQKCSKLDTAAPQSLEFLRTPFGGHLLVLESFLYKQEKA

Parental  VGDKVYW-KCRQHAELGCRGRAITRGLRATVMRGHCHAPDEQGLEARRQREKLPSKALPEGCGERKGPEG
          VGDKVYW..CRQHAELGC.GRAITRGLRATVMRGHCHAP.EQG.EA.RQREKLPS.ALPEG.GE..GPEG
Retrocopy VGDKVYW<ECRQHAELGCPGRAITRGLRATVMRGHCHAPNEQGMEAWRQREKLPSLALPEGLGEPQGPEG

Parental  PGGRVEEPLEGVGPWQCPEEPEPEPEPTPGLGLSKPAPEEEGPRALSLLSLPPKKRSILGLGQARPLEFL
          PGGRVEEPLEGVGPWQCPEEPEPEP..TPGL.LSKPAPEEEGPRALSLLSLPPKKRSILGLGQARPLEFL
Retrocopy PGGRVEEPLEGVGPWQCPEEPEPEP--TPGLVLSKPAPEEEGPRALSLLSLPPKKRSILGLGQARPLEFL

Parental  RTCYGGSFLVHESFLYKREKAVGDKVYWTCRDHALHSCRSRAITQGQRVTVMRGHCHQPDMEGLEARRQQ
          RTCYGGSFLVHESFL.KREKAVGDKVYWTCRDHALHSC.SRAIT.GQRVTVMRGHCHQPDMEGLEARRQQ
Retrocopy RTCYGGSFLVHESFLCKREKAVGDKVYWTCRDHALHSCWSRAITRGQRVTVMRGHCHQPDMEGLEARRQQ

Parental  EKAMETLQAGQDGPGSQVDTLLPGVDSLLYRRGPGPLTLTRPQPRKRAKVEDQELPTQPKALEGSPDEDQ
          EKAMETLQAGQDGPGSQVDTLL.GVDSLLYRRGPGPLTLTRP.PRKRAKVEDQELP.QP.A.EGSPDEDQ
Retrocopy EKAMETLQAGQDGPGSQVDTLLQGVDSLLYRRGPGPLTLTRPRPRKRAKVEDQELPIQPEAPEGSPDEDQ

Parental  DVDADPGGPEFLKTPLGGSFLVYESFLYRREKAAGEKVYWTCRDQA-RMGCRSRAITQGRRVTVMRGHCH
          D.DADPGG.EFLKTPLG.SFLVYESFLYRREKAAGEKVYWTCRDQA.RMGCRSRA.TQGRRV.VMR.HCH
Retrocopy DMDADPGGREFLKTPLGSSFLVYESFLYRREKAAGEKVYWTCRDQALRMGCRSRAMTQGRRVMVMRRHCH

Parental  PPDLGGLEALRQREKRPNTAQRGSP
          PPDLGGLEALR.RE..P..AQ..SP
Retrocopy PPDLGGLEALRKREHFPSLAQWDSP

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_3085 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000059122	1 retrocopy	retro_hsap_2890,
Nomascus leucogenys	ENSNLEG00000009480	2 retrocopies	retro_nleu_3085 , retro_nleu_628,