RetrogeneDB ID: retro_nleu_1378

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397291.1:9274189..9275571(-)
• Located in intron of: ENSNLEG00000001700

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_1378
CTGACCCGGAAGATCACGCTGAAGATGCTGCTGACGCTGATCTCCTCCCCCATGGACACTGTGACAGAGGCGAACATGGC
CATTGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTACACCCCAGAGTTCCAGGCCAAGAGGTGCAGAA
GGTCAAGAAGTTTGAAGAGGGGGGCTTCATCATGGACCCCATGGTGCTGAGCCCCTCGCACACTGTGGGTGATGTAATGG
AGCCGAAGATGCGGCATGGCTTCTCTGGCATCCCGATGACTGAGACGGGCATCATGCGCAGCAAGCTGGTGGGCATCGTC
ACCTCCTCGGACATCAACTTTCTTGCTGAGAAGGATCACAACACCCTCCTCAGTGAGGTGATGAAGCCAAGGATAGAGCT
GGTGGTGGCTCTAGCAGGCGTGACATTGAAAGAGGCAAATGAGATCCTGCAGTGTAGCAAGAAAGGGAAGCTGCCTATCA
TCAACGATCTGGATGAGCTGGTGGCCATCATCGCCCGCACCGATCTGAAGAGGAACCGAGACTACCTTCTGGCCTCCAAG
GATTCCCACGAGCAGCTGCTGTGGGGGGCAGCTGTGGGCACTCCTGCGGATGGCAAATACCTCCTGGACCTGCTCACCCA
GGCGGGCGTCAACGTCATAATCTTGGACTTATCCCAAGGGAACTCAGTGTATCAGATCGCCATAGTGCATTACATCAAAC
AGAAGTACCCCAACCTCCAGGTGACTGGGGGGAACGTGGTGACAGCAGCCCAGGGCAAGAACCTGATTGATGCTGGTGTG
GACGAGCTGTGCGTGGGGATGAGCTGTGGCTCCATCTGCATCACCCAAGAAGTGATGGCCTGCGGTTGGCCCCAGGGCAC
TGCTGTGTACAAGGTGGCCGAGTATGCTCAGCGCTTCGGTGTGCCCATTATATCCGGATGGTGACATCCAGACCGTGGGG
CACATGGTCAAGGCCCTGGAACTTGGAGCCTCCACAGTGATGATGGGTTCCCTGCTGGCTGCCACCACGGAGGCCCCCTG
TGAGTACTTCTCAGACGGGGTGCAGCTTAAGAAGTATCGGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCA
GCCGGAAACGATACTTCAGTGAGGGGGATAAGGTGAAGATAGCGCAGGGTGCCTCGTGTTCCATCCAGGACAAAGGTTAC
ACTCAGAAGTTCATGCCCTACCACATAGTGGGCATCCAGCACGGCTGCCAGGATATCGGGGCCACAGCCTGTCTGTCCTT
TGGTCCATGATGTACTCAGGAGAGCTCAAGTTTGAGAAGCAGACCGTGTCAGCCCAGACTGAGGGTGGTGTCCATGGCCT
GCACTTTTACGAGAAGCGGCTA

Alignment

ORF - retro_nleu_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTKKITLKT--PLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQAN-EVRKVKKYEQG-FITDPVV
          LT.KITLK....L.SSPMDTVTEA.MAIAMAL.GGIGFIHHN.TPEFQA..EV.KVKK.E.G.FI.DP.V
Retrocopy LTRKITLKMLLTLISSPMDTVTEANMAIAMALMGGIGFIHHNYTPEFQAK<EVQKVKKFEEGGFIMDPMV

Parental  LSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSRDIDFLKEEEHDCFLEEIMTKREDLVVAPA
          LSP...V.DV.E.K.RHGF.GIP.T.TG.M.S.LVGI..S.DI.FL.E..H...L.E.M..R..LVVA.A
Retrocopy LSPSHTVGDVMEPKMRHGFSGIPMTETGIMRSKLVGIVTSSDINFLAEKDHNTLLSEVMKPRIELVVALA

Parental  GITLKEANEILQRSKKGKLPIVNEDDELVAIIARTDLKKNRDYPLASKDTKKQLLCGAAIGTHEDDKYRL
          G.TLKEANEILQ.SKKGKLPI.N..DELVAIIARTDLK.NRDY.LASKD...QLL.GAA.GT..D.KY.L
Retrocopy GVTLKEANEILQCSKKGKLPIINDLDELVAIIARTDLKRNRDYLLASKDSHEQLLWGAAVGTPADGKYLL

Parental  DLLAQAGVDVVVLDSSQGNSIFQINMIKYIKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSI
          DLL.QAGV.V..LD.SQGNS..QI....YIK.KYPNLQV.GGNVVTAAQ.KNLIDAGVD.L.VGM..GSI
Retrocopy DLLTQAGVNVIILDLSQGNSVYQIAIVHYIKQKYPNLQVTGGNVVTAAQGKNLIDAGVDELCVGMSCGSI

Parental  CITQEVLACGRPQATAVYKVSEYARRFGVPVIA-DGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGE
          CITQEV.ACG.PQ.TAVYKV.EYA.RFGVP.I..DG.IQ.VGH..KAL.LGASTVMMGSLLAATTEAP.E
Retrocopy CITQEVMACGWPQGTAVYKVAEYAQRFGVPIIS>DGDIQTVGHMVKALELGASTVMMGSLLAATTEAPCE

Parental  YFFSDGIRLKKYRGMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQ
          Y.FSDG..LKKYRGMGSLDAM.K..SS..RYFSE.DK.K.AQG.S...QDKG...KF.PY.I.GIQH.CQ
Retrocopy Y-FSDGVQLKKYRGMGSLDAMEKSSSSRKRYFSEGDKVKIAQGASCSIQDKGYTQKFMPYHIVGIQHGCQ

Parental  DIGA-KSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRL
          DIGA..SL.....MMYSGELKFEK.T.SAQ.EGGVH.LH.YEKRL
Retrocopy DIGA<HSLSVLWSMMYSGELKFEKQTVSAQTEGGVHGLHFYEKRL

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_1378 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,