RetrogeneDB ID: retro_nleu_1573

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:21312203..21313734(-)
• Located in intron of: ENSNLEG00000015182

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT11
• Ensembl ID: ENSNLEG00000004613
• Aliases: None
• Description: None

Sequence

>retro_nleu_1573
CTCAAGGGGTCTGGACCCCATGGACCATTTCCAAAACAATTCTATTCTTGTTTCACTCAAGGTCCAAGTCTATTACTAGA
GCCACAGTTCGAAGCAAACAAAATCGGATGATGGTGATAGTCATATTGAAGATCCAGATAAAAGGCCCACTGGAAATGGT
CCTCTGAACTAGGCATGATTTTTAATGAAAGGTGCTCAGGAGTTGAGAGACTTGCGCTATCAAAAACATGCTTTTAATAT
GCTTATCAGTAATTGCAGGCTACCACAGAGATGTGCCAGGGACAAAGAATCCAGCATTTAAAGTCCTACCACCTGACCTG
CCAGTTGCTAACATTGTTATCTGTTTCCACAATGAAGCTTTTTCTGCCTGTCTCCAGACGCTGCACATTGTCATAAATTG
CATGCCAGCAAACCTGCTTCATGAAATCATCCTCATGGATGTTGTTAGTGACCTTGATGATTTGAAAGGAGAACAAGATG
AATATGTCCAAAAATACCTCCCTGGAAAAATTAAGGTATAAGAAATATAAAGTGTGAGGGATTGATTTCAAGGAAGAATG
AGTGTAGCAGTCCACACAACAGAAGTCCTTGTGTTCCTAGACAGCCACGTGAAGTGAATGTGACATGGCTGCAGCCCTTG
CTGGCTGTCATCTGTGTGGACTGGCAGACCATGATGTTCTCAGTGATTGACATCATTAGTACCAACACGCTAGCCTACAG
CTCATCCTCTGGTCCGTGGAGGATTCAACTGAGGGCTGCACTTCAAATAGGAGCTTGTTTCCCTTTCTGAGCTAGGATGA
GCAGAAAAAGCCACAGCACCAACAAAGTCACCAATAATGACCGGAGGATTGCTTGCCAGGAACAGACAGTATTTCCATGA
ACTTGGACAATATGATACTGGCATGGATATCTGGAGAGGAGAAAATTTGGAAAGATCATTTCAGATCTGGGTGTGTGGAG
GTAAGTTCTTCATCATGCCTTGCTCTACAGTAGGACACATTTTCCAAAAAAGGTGACCATATGGATCTCCTGAAGGCCAG
GACACCATGAACACAACTCTTTGAGGCTGGCACATGTCTGGCTGGATGAATAAAGTGGCAGTATTTTTCCTTAAGACTTA
ATCTGAAGAGGAAAAGCTATGGAACTATCAGTGAACAAGTGGAATTGAGAAAGAAGTTAGGATGCAAATCATTTAAATGG
TATTTGGATAATATTTACCCAGAGACGCAGATATCTGGGACCCATGCCAAATCCGAGCAACCCACTTTTATCATTAGAGG
GCCAAAATGCCCCAGTCCTTCAACTTGGAAGGCTGTATCACCTCCATACCAACAAATGTCTGGTGGCTCAGGGATGCCCA
AGTCAGAAAGGAGGCCTACCAGTGCTTAAGGCCTGTGAGCATGGGGACCCAAATCAGATCTGGATTGATAATGAAGAGCA
TGAATTGGTTTTAAACCATCTTCTTTGTCTAGGTATGACAGAAACTAGCTCATCAGACCCACCACGACTCATGGAGTGCC
ATGGGTCAGGC

Alignment

ORF - retro_nleu_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 84.87 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  VKGSGPHGPSPKKFYPRFTRGPSRVLEPQFKANKIDDVIDSHVEDPEKGHLKFSSELGMIFNERDQELRD
          .KGSGPHGP.PK.FY..FT.GPS..LEPQF.ANKI.....S......K.H.K.SSELGMIFNER......
Retrocopy LKGSGPHGPFPKQFYSCFTQGPSLLLEPQFEANKIG*W**SY*RSR*KAHWKWSSELGMIFNERCSGVER

Parental  LGYQKHAF-NMLISNRLGYHRDVPDTRNAACQEKFYPPDLPSASVVICFYNEAFSALLRTAHSVIDRTPA
          L...K..F.....S...GYHRDVP.T.N.A...K..PPDLP.A..VICF.NEAFSA.L.T.H.VI...PA
Retrocopy LALSKTCF<LICLSVIAGYHRDVPGTKNPAF--KVLPPDLPVANIVICFHNEAFSACLQTLHIVINCMPA

Parental  HLLHEIILVDDDSDFDDLKGELDEYVQKYLPGKIKV-IRNTKREGLI-RGRMIGAAHATGEVLVFLDSHC
          .LLHEIIL.D..SD.DDLKGE.DEYVQKYLPGKIKV.IRN.K.EGLI..GRM..A.H.T.EVLVFLDSH.
Retrocopy NLLHEIILMDVVSDLDDLKGEQDEYVQKYLPGKIKV<IRNIKCEGLI>QGRMSVAVHTT-EVLVFLDSHV

Parental  -EVNVMWLQPLLAAIREDQHTVVCPVIDIISADTLAYSSS-PVVRGGFNWGLHFKWDLVPLSELGGAEGA
          .EVNV.WLQPLLA.I..D..T....VIDIIS..TLAY.SS.P.VRGGFN.GLHFK..LV.LSELG.AE.A
Retrocopy <EVNVTWLQPLLAVICVDWQTMMFSVIDIISTNTLAY-SS>PLVRGGFN*GLHFK*ELVSLSELG*AEKA

Parental  TAPIKSPTMAGGLFAMNRQYFHELGQYDSGMDIWGGENLEISFRIWMCGGKLFIIPCSRVGHIFRKRRPY
          TAP.KSP.M.GGL.A.NRQYFHELGQYD.GMDIW.GENLE.SF.IW.CGGK.FI.PCS.VGHIF.KR.PY
Retrocopy TAPTKSPIMTGGLLARNRQYFHELGQYDTGMDIWRGENLERSFQIWVCGGKFFIMPCSTVGHIFQKR*PY

Parental  GSPEGQDTMT-HNSLRLAHVWLDE-YKEQYFSLRPDLKTKSYGNISERVELRKKLGCKSFKWYLDNVYPE
          GSPEGQDTM..HNSLRLAHVWLDE..K.QYFSLR..LK.KSYG.ISE.VELRKKLGCKSFKWYLDN.YPE
Retrocopy GSPEGQDTMN<HNSLRLAHVWLDE<IKWQYFSLRLNLKRKSYGTISEQVELRKKLGCKSFKWYLDNIYPE

Parental  MQISGSHAKPQQPIFVNRGP-KRPK-VLQRGRLYHLQTNKCLVAQGRPSQKGGLVVLKACDYSDPNQIWI
          .QISG.HAK..QP.F..RGP.K.P..VLQ.GRLYHL.TNKCLVAQG.PSQKGGL.VLKAC...DPNQIWI
Retrocopy TQISGTHAKSEQPTFIIRGP<KMPQ<VLQLGRLYHLHTNKCLVAQGCPSQKGGLPVLKACEHGDPNQIWI

Parental  YNEEHELVLNSLLCLDMSETRSSDPPRLMKCHGSG
          .NEEHELVLN.LLCL.M.ET.SSDPPRLM.CHGSG
Retrocopy DNEEHELVLNHLLCLGMTETSSSDPPRLMECHGSG

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_1573 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001121	1 retrocopy	retro_chof_1535,
Homo sapiens	ENSG00000178234	1 retrocopy	retro_hsap_402,
Gorilla gorilla	ENSGGOG00000008784	1 retrocopy	retro_ggor_399,
Nomascus leucogenys	ENSNLEG00000004613	1 retrocopy	retro_nleu_1573 ,
Nomascus leucogenys	ENSNLEG00000017019	1 retrocopy	retro_nleu_940,
Pan troglodytes	ENSPTRG00000019891	1 retrocopy	retro_ptro_308,