RetrogeneDB ID: retro_nleu_1126

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:29060388..29061847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH2
• Ensembl ID: ENSNLEG00000006743
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G1R4U5]

Sequence

>retro_nleu_1126
GACGGCCTCACCTACAACAACTTCCTGATTCTCCCAGGATTCATAGACTTCATAGCTGATGAGGTGGACCTGACCTCAGC
CCTAACCTGGAAGATCACGCTGAAGACGCCACTGATCTCCTCCCCCATGGACACTGTGACAGAAGCTGACATGGGTGTCG
CGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGCCAAGGAGGTGTGGAAGGTC
AAGAAGTTTAACGGAGCTTCATCATGGATCCCGTGGTACTGAGCCCCTCGCACACCGTGGGTGATATGCTGGAGGCCAAG
CTGCAGCATGGCTTCTCTGGCATCCCCATCACTGAGAGAGGCACCATGGGCAGCAAGCTGGTGGACATTGTCACCTCCCG
AGACGTCAACTTTCTTGCTGAGAAGGACCACATCACCCTCCTCAGTGAGGTGACGACACCAAGGATTGAGCTGGTGGTGG
CTCCAGCAGGTGTGGTGCTGAAAGAGGCAAATGAGATCCTGCAGCCGTAGCAAGAAAGGGAAACTGCCTATCATCAGTGA
TCGCAATGAGCTGGTGGCCATCATCGCCCACACCAACATGAAGAAGAACTGAGACTACCCTCTGGCCTCCAAGGATTCCC
ACAGGCAGCTGCTGTGCAGGGCAGCTGTGGGCACCTGTGAGGATGACAAATACCGCCTGGACCTGCTCACCCAGGTGGGT
GTCAACATCATAGTCTTGGACTTGTCCCAAGGGAACTCATCGTATCAGATCGCCATGGTGCATTACATCAAACAGAAGTA
CCCCCACCTCCAGGTGATTGGGGGCAACAAGGTGACAGCAGCCCAGGCCAAGAACCTGACTGACCCTTGTGTGGAAGGGC
TGCATGTGGGCATGGGCTGCAGCTCCATCTGCATCACCCAGGAAGTGATGGCCTATGGTCGGCCCCAGGGCACTGCTGTG
TACAAAGTGGCCGAGTATGCCCGGCGCTTTGGTGTGCCTATCATAGCCGATGGCGGCATCCAGGCTATGGGGCACGTGGT
CAAGGCCCTGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCCTGCTGGCCGCCACCACAGAGGTCCTCAGTGAGTACT
TCTTCTCAGATGGGGTGTGGCTCAAGAAGTACCGGGGCATGGGCTCACTGGATGCCCTGGAGAAGAGCAGCAGCAGCCAG
AAACAATACTTCATCGAGGGGTATAAGGTGAAGATTGCGCAGGGTGTCTCCAGCTCCATCCAGGACAAAGGGTCCGTTCA
GAACTTTGTGCCCTACCTCATAGCAGGCATCCAGCACGGCTGTCAGGATACCGGGGCCCGCAGCCTGTCTGTCCTTTGGT
CCATTTTGTACTCAGGAGAGCTCAAAGTTTCAGAAGTGGACCATGTTGGCCCAGATCAGAGGTGGCGTCCAAGGCCTGCT
CTCTTATAAGAAGCGGCTA

Alignment

ORF - retro_nleu_1126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 94.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTP
          DGLTYN.FLILPG.IDF.AD.VDLTSALT.KITLKTPL.SSPMDTVTEA.M..AMAL.GGIGFIHHNCTP
Retrocopy DGLTYNNFLILPGFIDFIADEVDLTSALTWKITLKTPLISSPMDTVTEADMGVAMALMGGIGFIHHNCTP

Parental  EFQANEVRKVKKYE-QGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSRDIDFL
          EFQA.EV.KVKK.....FI.DPVVLSP...V.D..EAK..HGF.GIPIT..G.MGS.LV.I..SRD..FL
Retrocopy EFQAKEVWKVKKFN<RSFIMDPVVLSPSHTVGDMLEAKLQHGFSGIPITERGTMGSKLVDIVTSRDVNFL

Parental  KEEEHDCFLEEIMTKREDLVVAPAGITLKEANEILQ-RSKKGKLPIVNEDDELVAIIARTDLKKNRDYPL
          .E..H...L.E..T.R..LVVAPAG..LKEANEILQ.RSKKGKLPI.....ELVAIIA.T..KKN.DYPL
Retrocopy AEKDHITLLSEVTTPRIELVVAPAGVVLKEANEILQ>RSKKGKLPIISDRNELVAIIAHTNMKKN*DYPL

Parental  ASKDTKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVVLDSSQGNSIFQINMIKYIKEKYPNLQVIGGNVV
          ASKD...QLLC.AA.GT.EDDKYRLDLL.Q.GV...VLD.SQGNS..QI.M..YIK.KYP.LQVIGGN.V
Retrocopy ASKDSHRQLLCRAAVGTCEDDKYRLDLLTQVGVNIIVLDLSQGNSSYQIAMVHYIKQKYPHLQVIGGNKV

Parental  TAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAK
          TAAQAKNL.D..V..L.VGMG..SICITQEV.A.GRPQ.TAVYKV.EYARRFGVP.IADGGIQ..GH..K
Retrocopy TAAQAKNLTDPCVEGLHVGMGCSSICITQEVMAYGRPQGTAVYKVAEYARRFGVPIIADGGIQAMGHVVK

Parental  ALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSG
          ALALGASTVMMGSLLAATTE...EYFFSDG..LKKYRGMGSLDA..K..SSQ..YF.E..K.K.AQGVS.
Retrocopy ALALGASTVMMGSLLAATTEVLSEYFFSDGVWLKKYRGMGSLDALEKSSSSQKQYFIEGYKVKIAQGVSS

Parental  AVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGEL-KFEKRTSSAQVEGGVHSLHSYEKRL
          ..QDKGS...FVPYLIAGIQH.CQD.GA.SL.......YSGEL.KF.K.T..AQ..GGV..L.SY.KRL
Retrocopy SIQDKGSVQNFVPYLIAGIQHGCQDTGARSLSVLWSILYSGEL>KFQKWTMLAQIRGGVQGLLSYKKRL

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_1126 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009844	1 retrocopy	retro_fcat_1377,
Homo sapiens	ENSG00000178035	1 retrocopy	retro_hsap_697,
Gorilla gorilla	ENSGGOG00000013245	1 retrocopy	retro_ggor_594,
Mus musculus	ENSMUSG00000062867	1 retrocopy	retro_mmus_3158,
Nomascus leucogenys	ENSNLEG00000006743	7 retrocopies	retro_nleu_1126 , retro_nleu_1371, retro_nleu_1378, retro_nleu_1591, retro_nleu_2183, retro_nleu_2188, retro_nleu_359,
Nomascus leucogenys	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
Pongo abelii	ENSPPYG00000013884	1 retrocopy	retro_pabe_528,
Pan troglodytes	ENSPTRG00000014908	1 retrocopy	retro_ptro_501,
Rattus norvegicus	ENSRNOG00000031965	1 retrocopy	retro_rnor_1523,
Tursiops truncatus	ENSTTRG00000017349	2 retrocopies	retro_ttru_1148, retro_ttru_1665,