RetrogeneDB ID: retro_nleu_1817

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397311.1:16082650..16083515(-)
• Located in intron of: ENSNLEG00000009103

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSNLEG00000000323
• Aliases: None
• Description: None

Sequence

>retro_nleu_1817
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCACAGTGTAGCCACACAGAAGGAAAAGGTTGAAGTAATATCTCC
CGAGAAGTTCAAAACAAGATTACAGAAAGAAAATGAGATTTTCTGCATGCAACAAGATACCCATGGGTTCTTAAATTACC
TACTAAATACAATTGCTGATATTCTATAAGAAGAGAGAACGCAGGATAAACAAAATGGTCACGTACCAAATGGTAATATT
GATACTGAAAATAACAACAGCACACCAGACCCAATGTAGGTTCATGAAATTTTTCAGAAAACATTAACTAATGAAACTAG
ATGTATTACTTGTGAAACTATAAGAGCAAAGATGAAGATTTTAAAGAACTTCCTGTGATATAGAACAAAATACATCAGTT
ATTCACTGTTTAAGGGTTTTTAACACAGAAACTCTATGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTGGCAAATA
GGAAGCACACGAATGAAAGTTTAAAAAGCACCCATGATTATAGCTCTACATCTGAAAAGATTTAAATATACGGATTAAAT
TCACCGATGTACGAAACTTTCTTACTAGGTAGTTTTTCGTTTAGAACTTTGTCTGTGTAACACTTCAGGGGATGCAACCA
ATCCAGACAGAATGCACGACCTTGTTGCTATTATGATTTACTGTGGAAGTGGTCACAGGTGAGGCCATTATATTGTAATA
GTTAAGAATCAAGATTTCTGCTTGTTCTTTGATGACACTGTAGAAAAAAATGAATTCACAAATTACTGAAGAATTCTACG
TATTGACCTCAGATATCGCAAAGAACTCAGAGTCTGGTTACATTCTTTTCTATTAGTCTCGGAAC

Alignment

ORF - retro_nleu_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.47 %
• Parental protein coverage: 82.82 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQ
          ....L.C.A..FHS.ATQK.KV.VI.P.KF.TRL.KENE.F...MQQD.H.FLNYLLNTIADIL.EER.Q
Retrocopy RRKILMCSATFFHSVATQKEKVEVISPEKFKTRLQKENEIF--CMQQDTHGFLNYLLNTIADIL*EERTQ

Parental  EKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETI-SSKDEDFLDL-SVDVEQNTSITH
          .KQNG..PNGNID.ENNNSTPDP..VHEIFQ.TLTNETRC.TCETI..SKDEDF..L.S.D.EQNTS..H
Retrocopy DKQNGHVPNGNIDTENNNSTPDPM*VHEIFQKTLTNETRCITCETI<KSKDEDFKEL<SCDIEQNTSVIH

Parental  CLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKK-LPMILALHLKRFKYMDQLHRYTKLSYRVVFPLE
          CLR.F.NTETL.SEY..YCEEC..K.EAH...K.KK..PMI.ALHLKRFKY.D..HR.TKLSY.VVF.LE
Retrocopy CLRVF-NTETL*SEYRHYCEECCGK*EAHE-*KFKK<APMIIALHLKRFKYTD*IHRCTKLSY*VVFRLE

Parental  LRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEK-IDAQAIEEFYGLTS
          L.L.NTSGDATNPDRM.DLVA....CGSG...GHYI.IVK..DF.L.F.DD.VEK....Q..EEFY.LTS
Retrocopy LCLCNTSGDATNPDRMHDLVAIMIYCGSGHR*GHYIVIVKNQDFCLFF-DDTVEK>MNSQITEEFYVLTS

Parental  DISKNSESGYILFYQSRD
          DI.KNSESGYILFY.SR.
Retrocopy DIAKNSESGYILFY*SRN

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_1817 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817 , retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,