RetrogeneDB ID: retro_nleu_2350

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397347.1:3554952..3555707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR4
• Ensembl ID: ENSNLEG00000014641
• Aliases: None
• Description: None

Sequence

>retro_nleu_2350
TCTGCTGCAAACAGTGATGACAACAACCTCTTCATCTATGACTGCAGTGCTGCAGAATAGTCACAAGAAAATAAAGGGGA
GGATGGGCTGCCCTTGGTCTGGGGGAGTGGCATGATTCTGGCATCCACCTCCAAGTCTGGCAGCTATTTTGCTTTAACAG
ATGACCACAAGCATCTGATTCTTTTCCATACAAAACCATGGCAATGTCTGAGTGTCAGGACCATGGCAAGGAGGTGTATG
GCCCTGACCTTACAGCCTCTGAGGTGAAGGTCTTGGTGGCTGACAAATCTGGAGATGTGTACTCCTTTTTGGTTTCAGAG
CCACATAGATGCGGCAGACTTGACCTGGCACACCTGTCAATGTTGTTAGAGGTGACTGTGAGTCCTGATAACTGCTTCAT
CCTCACTGCCAACCAGGATGAGAAGATCCAGGTCAGCTAGGCCACAGCGCCTCACAGTATCGAGTCCTTCTGCCTCAGGC
ACACGTAGTTTGTGAGCTGCATCTCTGTGGTGCCCACTCAGCCCGAACTGTTTCTTGTCCTCCTCCAGGGACTGCACTCT
TAGGCTCTGGGAGTACAGAAGTGGCCATCAACTGCACTGCTCTCACCTGGCCAGTCTGCAAGGGCTGATGGACCCCTGGG
ACACCAGAGGTTTGTCACATCCGGGATCATGTTCTGGTGTTAGGAGAACTGCATGACGCTTCTGTGCAACTGTATTCCTG
TAATCTACATCTTCCAGCTTGATATTCTCAGACAG

Alignment

ORF - retro_nleu_2350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.37 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STASSDDDSLFIYDCSAAEKKSQENKGEDA-PLDQGSVAILASTFSKSGSYFALTDDSKRLILFRTKPWQ
          S.A.SDD..LFIYDCSAAE..SQENKGED..PL..GS..ILAST.SKSGSYFALTDD.K.LILF.TKPWQ
Retrocopy SAANSDDNNLFIYDCSAAE*-SQENKGEDGLPLVWGSGMILAST-SKSGSYFALTDDHKHLILFHTKPWQ

Parental  CLSVRXXXXXXXXLTF-IASEEKVLVADKSGDVYSFSVLEPHGCGHLELGHLSMLLDVAVSPDDCFILTA
          CLSVR........LT...ASE.KVLVADKSGDVYSF.V.EPH.CG.L.L.HLSMLL.V.VSPD.CFILTA
Retrocopy CLSVRTMARRCMALTL<TASEVKVLVADKSGDVYSFLVSEPHRCGRLDLAHLSMLLEVTVSPDNCFILTA

Parental  DRDEKIRVSWAAAPHSIESFCLGHTEFVSRISVVPTQPGL-LLSSSGDGTLRLWEYRSGRQLHCCHLASL
          ..DEKI.VS.A.APHSIESFCL.HT.FVS.ISVVPTQP.L..LSSS.D.TLRLWEYRSG.QLHC.HLASL
Retrocopy NQDEKIQVS*ATAPHSIESFCLRHT*FVSCISVVPTQPEL>FLSSSRDCTLRLWEYRSGHQLHCSHLASL

Parental  QELVD-PQAPQRFAASRIAFWCQENCVALLCDGTPVVYIFQLDACRQ
          Q.L.D.P...QRF..S.I.FWC.ENC..LLC...PV.YIFQLD..RQ
Retrocopy QGLMD<PLGHQRFVTSGIMFWC*ENCMTLLCNCIPVIYIFQLDILRQ

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_2350 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160193	1 retrocopy	retro_hsap_4905,
Gorilla gorilla	ENSGGOG00000016652	1 retrocopy	retro_ggor_3063,
Nomascus leucogenys	ENSNLEG00000014641	1 retrocopy	retro_nleu_2350 ,
Pongo abelii	ENSPPYG00000011458	1 retrocopy	retro_pabe_3814,