RetrogeneDB ID: retro_nleu_2469

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397359.1:64297..64883(+)
• Located in intron of: ENSNLEG00000008227

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKACB
• Ensembl ID: ENSNLEG00000009888
• Aliases: None
• Description: None

Sequence

>retro_nleu_2469
TTCCAGTACCTGCACCCGCTCGACCTCATCCACCGCGGCCTGAAGCCCGAGAATCTTCTCCTCGACCTGCAGGGCTACCT
GCGGGTCCCGGACTTTGGTTTCGCCAAGCGCGTGAAGGGCCGCACTTGGACCTTTTGGGGACCCCGGTGTACCTGGCCCC
CGAGATCATCCTGAGCAAAGGCTACAGCAAGGCCGTGGACTGGTGGGCCCGAGGGGTGCTCATCTAGGAGATGGCCGTGG
GCTTCCCACCCTTCCACGCCCACCAGCCCATCCAGGTCTACGAGAAGATCGTCTCTGGGAGGGCGCGCGGTTTCCCTCCA
AACTCAGCTCTGACCTCAAGGATCTGCTGCGGCTGCTGCAGGTGGACCTCACCAAGCGCTTCGGAAATCTCAGGAACGGG
GTTGGCGACACCAAGAACCACAGGTTCGCCACAACCAACTGGATCGCCATCTGTGAGAAGAAGGTGGAAGCTCCCTTAAT
CCCGAAGTACTCAGGCCCTGGGGATGCCAGTAACTTTGACAACTACGAGGAGGAAGAGCTCTGGATCTCCATCAGTGAGA
AGTGCGCCAAGGAGTTTTCGGAGTTT

Alignment

ORF - retro_nleu_2469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.5 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FEYLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWT-LCGTPEYLAPEIILSKGYNKAVDWW
          F.YLH.LDLI.R.LKPENLL.D.QGY..V.DFGFAKRVKGRTWT.L.GTP.YLAPEIILSKGY.KAVDWW
Retrocopy FQYLHPLDLIHRGLKPENLLLDLQGYLRVPDFGFAKRVKGRTWT<LLGTPVYLAPEIILSKGYSKAVDWW

Parental  ALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVR-FP-SHFSSDLKDLLRNLLQVDLTKRFGNLKNGVSD
          A.GVLI.EMA.G.PPF.A.QPIQ.YEKIVSG..R.FP.S..SSDLKDLLR.LLQVDLTKRFGNL.NGV.D
Retrocopy ARGVLI*EMAVGFPPFHAHQPIQVYEKIVSGRARGFP<SKLSSDLKDLLR-LLQVDLTKRFGNLRNGVGD

Parental  IKTHKWFATTDWIAIYQRKVEAPFIPKFRGSGDTSNFDDYEEEDIRVSITEKCAKEFGEF
          .K.H..FATT.WIAI...KVEAP.IPK..G.GD.SNFD.YEEE....SI.EKCAKEF.EF
Retrocopy TKNHR-FATTNWIAICEKKVEAPLIPKYSGPGDASNFDNYEEEELWISISEKCAKEFSEF

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_2469 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
Macaca mulatta	ENSMMUG00000003457	1 retrocopy	retro_mmul_186,
Nomascus leucogenys	ENSNLEG00000008541	1 retrocopy	retro_nleu_1293,
Nomascus leucogenys	ENSNLEG00000009888	1 retrocopy	retro_nleu_2469 ,
Pongo abelii	ENSPPYG00000001209	1 retrocopy	retro_pabe_61,
Rattus norvegicus	ENSRNOG00000004978	1 retrocopy	retro_rnor_519,
Tarsius syrichta	ENSTSYG00000000380	2 retrocopies	retro_tsyr_1640, retro_tsyr_1802,