RetrogeneDB ID: retro_nleu_1094

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:20436258..20438054(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000010003
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX43
• Ensembl ID: ENSNLEG00000001209
• Aliases: None
• Description: None

Sequence

>retro_nleu_1094
AGAGGCAGTGGCTGGAGTGGCCCCTTCGGCCATCAGGGACCGAGAGCGGCAGGCTCCCGTGAACCACCACTCTGCTTTAA
AATAAAGAATATGGTTGGTGCGGTCATTGGTCACAGTGGATCAAAAATAAAATATCTACAACATTCGACAAACACTAAAA
TATAGATCATAAAAGGGGAATCTGAAGCAAAAGTCAGAATTTTTGGCAATAGGGAAATGAAAGCAAAGGCCAAAGCGGCT
ACAGAAACACTTACTAGAAAACAAGAAAGCTACAACTCAGAATCCAGTGTGGATAATGCTGCATCCCAATCCCCTATTGG
AAGAAATCTAGGCAGAAATGACGTTGTTGGAGAAGCTCAGCCATTGTCAAATTGGGATCGCATTAGGGCAGCAGTCGTGG
AGTACGAAAAGAGAAAATGGGCAGATTTACCACCAGTTAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTGCATG
TCTGAAATGCAGGTGATTAACTGGAGAAAGGAAAATTTCAACATAATGTGTGATGACTTGAAAAGTGGTGAAAAGCGTCT
CATCCCAAAACCAACTTGTAGGTTTAAAGACGCTTTTCAGCAATACCCTGATTTTCTGAAAAGCATAACAAGGGTAGGGA
TTGTAAAGCCAACGCCAATTCAGTCACAGGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGAAGTTGCACAAACC
GGAACAGGGAAAACACTGTCCTATTTAATGCCTGGGTTTATTCCTCTTGATTCTCAACCAATATCTAGAGAGCAAAGGAA
TGGGCCTGGGATGCTAGTCCTTACACCCACTAGAGAGTTGGCTCTTCAGGTGGAAGCTGAATGTTCAAAGTATTCATATA
AAGGTCTCAAAAGCATTTGCATATATGGTGGTAGAAATAGAATTGGATAAATAGAAGATATTAGCAAAGGTATAGATATC
ATTATTGCAACTCCTGGGAGGCTGAATGACCTACAAATGAATAATTCTGTCAACCTAAGAAGCATAACCTACTTGGTTAT
AGATGAGGCAGATAAAATGCTGGATATGGAATTTGAACCCCAGATAATGAAGATTTTATTAGATGTGCGCCCAGACCGAC
AGACTGTTATGACAAGTGCAACTTGGCCAGATACTGTACGTCAACTAGCACTTTCTTATTTGAAAGATCCTATGATTGTT
TATGTTGGTAATCTGAATCTAGTTGCTGTAAATACAGTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAACGAGC
TCTCACCCAAGAATTCGTAGAGAACATGTCACCCAATGACAAAGTCATCATGTTTGTCAGCCAAAAACATGTTGCTGATG
ACTTGTCAAGCGACTTCAATATCCAAGGCATATCTGTAGAATCATCACATGGCAACAGTGAACAGAGTGATCAAGAGCGA
GCATTAGAGGACTTTAAAAGTGGAAACATAAAGATACTGATTGCAACTGATTTAGTATCCCGAGGTCTTGATCTTAATGA
TGTCACACATGTATATAATTACGATTTCCCAAGGAATATTGAAGTATATGTACACAGAGTAGGGTACATTGGATGGGCAG
GAAAGACTGGCACATCAGTTACCCTCATCACTCAGATTCGAAAATGGCCGGTGAATTGATTAAAATTCTGGACAGAGCAA
ATCAGAGTGTTCCGGAAGATCTTGTAGTAATAGCTGAGCAATACAAGTTAAATCAACAAAAGAGGGACACAGAAACACAA
TGAAGAAAACCTCAACAAAGATGCAAGGAGTTTTAT

Alignment

ORF - retro_nleu_1094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.91 %
• Parental protein coverage: 92.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGGRWRGPSRPPEAVAAGHEELPLCFALKNHFVGAVIGRGGSKIKNIESTTNTTIQIIQEQPESLVKIFG
          RG..W.GP.......AAG..E.PLCF..KN..VGAVIG..GSKIK.....TNT.I.II....E..V.IFG
Retrocopy RGSGWSGPFGHQGPRAAGSREPPLCFKIKN-MVGAVIGHSGSKIKYLQHSTNTKI*IIKGESEAKVRIFG

Parental  SKAMQTKAKAVIDNFVKKLEENYNSECGVD--CIQPAVGKDGSTDNNVVAGDRPLIDWDQIREEGLKWQK
          ...M..KAKA.......K..E.YNSE..VD....Q...G......N.VV....PL..WD.IR.......K
Retrocopy NREMKAKAKAATETLTRK-QESYNSESSVDNAASQSPIGRNLGR-NDVVGEAQPLSNWDRIRAAVVEYEK

Parental  TKWADLPPIKKNFYKESTATSAMSKVQADSWRKENFNITWDDLKDGEKRPIPNPTCTFDDAFQCYPEVME
          .KWADLPP.KKNFY.ES.ATS.MS..Q...WRKENFNI..DDLK.GEKR.IP.PTC.F.DAFQ.YP....
Retrocopy RKWADLPPVKKNFYIESKATSCMSEMQVINWRKENFNIMCDDLKSGEKRLIPKPTCRFKDAFQQYPDFLK

Parental  TIKKAGFPKPTPIQSQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIHLDLQPTLKGQRNRPGMLVLTPT
          .I...G..KPTPIQSQAWPI.LQGIDLI.VAQTGTGKTL.YLMPGFI.LD.QP....QRN.PGMLVLTPT
Retrocopy SITRVGIVKPTPIQSQAWPIILQGIDLIEVAQTGTGKTLSYLMPGFIPLDSQPISREQRNGPGMLVLTPT

Parental  RELALQVEGECCKYSYKGLRSVCVYGGGNRDEQIEELRKGVDIIIATPGRLNDLQMNNFVNLKNITYLVL
          RELALQVE.EC.KYSYKGL.S.C.YGG.NR...IE...KG.DIIIATPGRLNDLQMNN.VNL..ITYLV.
Retrocopy RELALQVEAECSKYSYKGLKSICIYGGRNRIG*IEDISKGIDIIIATPGRLNDLQMNNSVNLRSITYLVI

Parental  DEADKMLDMGFEPQIMKILLDVRPDRQTVMTSATWPHSVHRLAQSYLKEPMIVYVGTLDLVAVSSVKQNI
          DEADKMLDM.FEPQIMKILLDVRPDRQTVMTSATWP..V..LA.SYLK.PMIVYVG.L.LVAV..VKQNI
Retrocopy DEADKMLDMEFEPQIMKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYVGNLNLVAVNTVKQNI

Parental  IVTTEEEKWSHMQTFLQNMSSTDKVIVFVSRKAVVDHLSSDLILGNISIESLHGDREQRDREKALENFKT
          IVTTE.EK....Q.F..NMS..DKVI.FVS.K.V.D.LSSD.....IS.ES.HG..EQ.D.E.ALE.FK.
Retrocopy IVTTEKEKRALTQEFVENMSPNDKVIMFVSQKHVADDLSSDFNIQGISVESSHGNSEQSDQERALEDFKS

Parental  GKVRILIATDLASRGLDVHDVTHVYNFDFPRNIEEYVHRIGRTGRAGRTGVSITTLT-RNDWRVASELIN
          G...ILIATDL.SRGLD..DVTHVYN.DFPRNIE.YVHR.G..G.AG.TG.S..TL....D...A.ELI.
Retrocopy GNIKILIATDLVSRGLDLNDVTHVYNYDFPRNIEVYVHRVGYIGWAGKTGTSV-TLI<HSDSKMAGELIK

Parental  ILERANQSIPEELVSMAERFKAHQQKREMERKTERPQGRPKKFH
          IL.RANQS.PE.LV..AE..K..QQKR..E.....PQ.R.K.F.
Retrocopy ILDRANQSVPEDLVVIAEQYKLNQQKRDTETQ*RKPQQRCKEFY

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_1094 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007851	1 retrocopy	retro_amel_31,
Callithrix jacchus	ENSCJAG00000009966	2 retrocopies	retro_cjac_3639, retro_cjac_3640,
Equus caballus	ENSECAG00000017971	1 retrocopy	retro_ecab_7,
Felis catus	ENSFCAG00000031631	1 retrocopy	retro_fcat_583,
Homo sapiens	ENSG00000080007	1 retrocopy	retro_hsap_76,
Gorilla gorilla	ENSGGOG00000016092	1 retrocopy	retro_ggor_2889,
Microcebus murinus	ENSMICG00000017145	1 retrocopy	retro_mmur_1603,
Monodelphis domestica	ENSMODG00000018546	1 retrocopy	retro_mdom_14,
Mustela putorius furo	ENSMPUG00000004342	1 retrocopy	retro_mputfur_47,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094 ,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Oryctolagus cuniculus	ENSOCUG00000006338	2 retrocopies	retro_ocun_1061, retro_ocun_227,
Otolemur garnettii	ENSOGAG00000013660	1 retrocopy	retro_ogar_227,
Procavia capensis	ENSPCAG00000005962	1 retrocopy	retro_pcap_151,
Pongo abelii	ENSPPYG00000016774	1 retrocopy	retro_pabe_39,
Pan troglodytes	ENSPTRG00000018344	1 retrocopy	retro_ptro_35,