RetrogeneDB ID: retro_nleu_2333

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397344.1:4404145..4404931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC25A
• Ensembl ID: ENSNLEG00000006390
• Aliases: None
• Description: None

Sequence

>retro_nleu_2333
CGGCTCTTCCGCTTTCCGTCCATGCCCTGCTGCATGCTCCGGCCCATTCTCGAGAGGCTGGAGCGGCCCCAGGACAGGGA
CATGCCCGTGCAGAATAAGTGGAGGCGGAGCGTGACCCCTCCTGAGGAGCAGCAGGAGGCTGAGGAAACTAAAGCCCGCA
TCCTCTGCTCAAAATCACTGTGTCACGATGAGATCCAGAATCTCCTGGACAGTGACCATCGAGAGCTGATTGGAGATTAC
TCTAAGGCCTTCCTCCTACAGACAGTAGATGGAAAGCATCAAGACGTCAAGTACATCTCACCAGAAACGATGGTGGCCCT
GTTGACGGGCAAGTTCAGCAACATCGTGGATAAGTTTGTGATTGTAGACTGCAGATACCCCTATGAGTATGAAGACGGGC
ACATCAAGACTGCGGTGAACTTGCCCCTGGAACGCGACGCCAAGAGCTTCCTGCTGCAGAGCCCCATCACACCCTGTAGC
CTGGACAAGAGAGTCATCCTCATTTTCCACTGTGAATTCTCATCTGAGCGTGGGCCCCGCATGTGCCGTTTCATCAGGGA
ACGAGACCATGCTGTCAACGACTACCCCAGCCTCTACTACCCCGAGATGTATATCCTGAAAGGCGGCCACAAGGAGTTCT
TCCCTTAGCACCCGAACTTCTGTGAACCCCAGGACTACCGGCCCATGAACCATGAGGCCTTCAAGGATGAGCTAAAGACC
TTCCGCCTCAAGACTCGCAGCTGGGCTGGGGAGCGGAGCCGGCGGGAGCTCTGTAGCCGGCTGCAG

Alignment

ORF - retro_nleu_2333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.68 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLFDSPSLCSSSTRSVLKRPERSQEESSPGNTKRRKSMSGASPKESTNPEKAHETLHQSLSLASSPKGTI
          .LF..PS......R..L.R.ER.Q....P...K.R.S.....P.E......A.ET....L...S.....I
Retrocopy RLFRFPSMPCCMLRPILERLERPQDRDMPVQNKWRRSVT--PPEEQ---QEAEETKARILCSKSLCHDEI

Parental  ENILDNDPRDLIGDFSKGYLFHTVAGKHQDLKYISPEIMASVLNGKFANLIKEFVIIDCRYPYEYEGGHI
          .N.LD.D.R.LIGD.SK..L..TV.GKHQD.KYISPE.M...L.GKF.N....FVI.DCRYPYEYE.GHI
Retrocopy QNLLDSDHRELIGDYSKAFLLQTVDGKHQDVKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEDGHI

Parental  KGAVNLHMEEEVEDFLLKKPIVPTD-GKRVIVVFHCEFSSERGPRMCRYVRERDRLGNEYPKLHYPELYV
          K.AVNL..E.....FLL..PI.P....KRVI..FHCEFSSERGPRMCR..RERD...N.YP.L.YPE.Y.
Retrocopy KTAVNLPLERDAKSFLLQSPITPCSLDKRVILIFHCEFSSERGPRMCRFIRERDHAVNDYPSLYYPEMYI

Parental  LKGGYKEFFMKCQSYCEPPSYRPMHHEDFKEDLKKFRTKSRTWAGEKSKREMYSRLK
          LKGG.KEFF......CEP..YRPM.HE.FK..LK.FR.K.R.WAGE.S.RE..SRL.
Retrocopy LKGGHKEFFP*HPNFCEPQDYRPMNHEAFKDELKTFRLKTRSWAGERSRRELCSRLQ

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_2333 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011077	2 retrocopies	retro_dord_336, retro_dord_783,
Nomascus leucogenys	ENSNLEG00000006390	1 retrocopy	retro_nleu_2333 ,
Otolemur garnettii	ENSOGAG00000002994	1 retrocopy	retro_ogar_3398,