RetrogeneDB ID: retro_nleu_285

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:34868660..34869619(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLS1
• Ensembl ID: ENSNLEG00000004830
• Aliases: None
• Description: None

Sequence

>retro_nleu_285
TCTCGACCATTGGTTGGTTGTACAGTGGTCAACATCAGTGCACAGAATCTCAAAGAGAGAAAACCTCACTTGGTCTTAGG
ACTTCTCTGGCAGATCATCTAAGTTGGTCTTTTTGATGATATTGAGATTTCTAGGAATGAAGCTCTGATCGCATTGCTAA
ATGAAGGTGAGGGACTAGAGGTACTAATGTAGCTTTCTCCTAAGGAATTACTGCTGTAATGGGTGAATTATCATCTGGCT
GATGCAGGGTGTTGTACCATCAACAACTTCAGCCAAGGCAATAAGGATTCAACAGCCTATTTTCATCTGCTTAAACAAAT
TGACCCTAAAGGTGACTGGGAATATGGACTTTTCAGTCCATCTTCAGGATTTCATAAGAAAAATAATCTGAAGTGTGCGG
ACTTATGCTCAAGAAGTAGACAAACTTGGCAGTAAACAGTTTGTTACTCCTGCAGATGTGGTTTCAGGCAATCCTAAACT
TAATTTAGCTTTCATAGTTAATCTGTTTAATACCTATCCATGCCTACACAAGTTGGATAATAATGACATCAATATAAACT
TATTGGAGGGAGAGAGCAAAGAAGAGAGGACATTTCAGAACTGGTGAATTCCTTGGAAATCAACCCATACATTAATCATT
TGTACAGTTACCTTGCAGATGCTTTAGCGATCTTTCCGCTCTATGATATGATCTGAGTGTCAGTCAACTGGATCCATGCC
AGCAAACCTCCTTATCCTGCCCTTGGAGGGAACATAAACGTTGATAACTAACTATGCAGTGGAACTTGGGAAGAATAAGG
CCAAATTCTCCTTCGCTGGCATTGCTGGGCAGGACCTAAATGAAGGGAATTCAACATTTATTCTGGCATTAGTTATGGCA
GCTGATGAGAAGGTACACGTTGAATATGTCATCAGATCTTGGAAAGGTTGAAAGTGTACTTTAAAAAGTGCAAATAAAA

Alignment

ORF - retro_nleu_285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.12 %
• Parental protein coverage: 51.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SASAIGCTVVNIGASDLKEGKPHLVLGLLWQIIKVGLFADIEISRNEALIALLNEGEELEELMKLSPEEL
          S....GCTVVNI.A..LKE.KPHLVLGLLWQII.VGLF.DIEISRNEALIALLNEGE.LE.LM.LSP.EL
Retrocopy SRPLVGCTVVNISAQNLKERKPHLVLGLLWQII*VGLFDDIEISRNEALIALLNEGEGLEVLM*LSPKEL

Parental  LLRWVNYHLTNAGWHTISNFSQDIKDSRAYFHLLNQIAPKDGEDGPAIAIDLSGINETNDLKRA-GLML-
          LL.WVNYHL..AG..TI.NFSQ..KDS.AYFHLL.QI.PK.G..........SG....N.LK.A.GLML.
Retrocopy LL*WVNYHLADAGCCTINNFSQGNKDSTAYFHLLKQIDPK-GDWEYGLFSPSSGFHKKNNLKCA<GLML<

Parental  QEADKLGCKQFVTPADVVSGNPKLNLAFVANLFNTYPCLHKPNNNDIDVNLLEGESKEERTFRNW-MNSL
          QE.DKLG.KQFVTPADVVSGNPKLNLAF..NLFNTYPCLHK..NNDI..NLLEGESKEERTF.NW..NSL
Retrocopy QEVDKLGSKQFVTPADVVSGNPKLNLAFIVNLFNTYPCLHKLDNNDININLLEGESKEERTFQNW<VNSL

Parental  GVNPYINHLYSDLADALVIFQLYEMIRVPVNWSHVNKPPYPALGGNMK-KIENCNYAVELGKNKAKFSLV
          ..NPYINHLYS.LADAL.IF.LY.MI.V.VNW.H..KPPYPALGGN....I.N........K.K..F...
Retrocopy EINPYINHLYSYLADALAIFPLYDMI*VSVNWIHASKPPYPALGGNIN>LITNYAVELGKNKAKFSFA--

Parental  GIAGQDLNEGNSTLTLALV-WQLMRRYTLNVLSDLGEGEKVNDEIIIK
          GIAGQDLNEGNST..LALV.WQLMRRYTLN..SDLG..E.V.....IK
Retrocopy GIAGQDLNEGNSTFILALV>WQLMRRYTLNMSSDLGKVESVL*KVQIK

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_285 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
Choloepus hoffmanni	ENSCHOG00000011426	1 retrocopy	retro_chof_203,
Nomascus leucogenys	ENSNLEG00000004830	1 retrocopy	retro_nleu_285 ,