RetrogeneDB ID: retro_nleu_2418

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:1488444..1489002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX39B
• Ensembl ID: ENSNLEG00000006094
• Aliases: None
• Description: None

Sequence

>retro_nleu_2418
AAGGTGTCCATGTTTTTCGGAGGCCTCTTCATCAAGAAGAATGAAGAATTGTTGATGAGTTGTCCTCATGTCATGGTGGG
GACCCCAGGTCAGATCGTAGCACTTATGCAGAACAGGAGCCTCAACCTGAAGAATGTGAAGCACTTTGTGCTGGATGAGA
TGCTGGGGTGGATGGACATGTGGCGGGACATGTGGGAGGCCTCCCACCTGATGTTCCAGCAGAAGCAGTGAATCATGTTC
AGTGCCACGCTGAGCAAGGAGATCTGGCCTGTGTGCAGGGAGTCCATGCAGGATCCCATGGAGGTGTTTGTGGATGACGA
GACCAAGTGCACGCTGCACGCACTGCAGCAGTACGACCTCAAGCTCAAGGACGCTGAGAAGAACCGCAAGCTTTTTGATC
TCCTGGACATGCTGGAATTTAAACAGGTGGCAATCTTCATCAAGCTGGTGCAGCCCTGCATGTCCCCGGCCCAGCTCCTC
ATGGAGCAGAACTTCCTGGCCATGGCCCAGGAGGAATGCCTGTCATGCTATCAGCAGTGCAAGGATTTCCAGCAGTGG

Alignment

ORF - retro_nleu_2418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.58 %
• Parental protein coverage: 54.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQE
          KV..FFGGL.IKK.EE.L...CPH..VGTPG.I.AL..N.SLNLK..KHF.LDE...ML...DM.RD..E
Retrocopy KVSMFFGGLFIKKNEELLM-SCPHVMVGTPGQIVALMQNRSLNLKNVKHFVLDE---MLGWMDMWRDMWE

Parental  IFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLD
          ........KQ..MFSATLSKEI.PVCR..MQDPME.FVDDETK.TLH.LQQY..KLKD.EKNRKLFDLLD
Retrocopy ASHLMFQQKQ*IMFSATLSKEIWPVCRESMQDPMEVFVDDETKCTLHALQQYDLKLKDAEKNRKLFDLLD

Parental  VLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQF
          .LEF.QV.IF.K.VQ.C...AQLL.EQNF.A.A..............QQ.
Retrocopy MLEFKQVAIFIKLVQPCMSPAQLLMEQNFLAMAQEECLSCYQQCKDFQQW

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_2418 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
Macropus eugenii	ENSMEUG00000008264	2 retrocopies	retro_meug_1623, retro_meug_288,
Nomascus leucogenys	ENSNLEG00000006094	1 retrocopy	retro_nleu_2418 ,