RetrogeneDB ID: retro_nleu_2188

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:7381694..7382970(-)
• 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_2188
ATTGGTTTCATTCACCACAACTGCACCCCAGAGTTTCAGGCCAACAAGGTGCAGAAGGTCAAGAAGTTTGAACAGGGCTT
CATCATGGACCCTGTGGTGCTGAGCCCCTCGCACACCGTGGGTGATGTGCTGGAGGCCAAGATGCCGCATGGCTTCTCTG
GCATCCCCACCACTGAGACCGGCACCATCGGCAGCAAGCTGGTGGGTATCGTCACCTTCCAAGATATAGACTTTCTTGCT
GAGAAGGACACCACCCTCCTCAGTGAGATGATGACGCCAAGGACCGAGCTGGTGGTGGCTCCAGCAGGCGTGACATTGAA
AGAGCAAATGAGATCCTGCAGCCTAGCAAGAAAGGGAAGCTGCCTGTCGTCAATGATCACGGTGAGCTGGTGGCCATCAT
CACCCGCACCGACCTGAAGAAGTACCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAGCAGCTGCTGTGCGGGGCAG
TTGTGGGCACCCGTGAAGATGACAAATTCCGCCTTGACCTGCTCACCCAGGCGGGCATCGATGTCATAGTCTTGGACTCG
TCCCAAGGGAACTTGGTGTATCAGATCGCCATGGTGCATTACATCAAACAGAAGTACCTTCACCTTCAGGTGATTGGGGG
GAACGTGGTGACAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGGACGGGCTGCACGTGGGCATGGGCTGCGGCT
CCATCTGCATCACCCAGGAAGTGATGTCCTGTGGTCACACCCACGGCACTGCTGTGTACAAGGTGGCCGAGTATGCCTGG
CGCTTTGGTGTGCCCCTCATAGCCGATGGCGGCATCCAGACCGTGGGGCACATGGTCAAGGCCCTGGCCCTTGGAGCCTC
CACAGTGATGATGGGCTCCTTGCTGGCCACCACCACGGAGGCCTCTGGCGAGTACTTCTTCTCAGACAGGGTGTGGCTCA
AGAAATACCGGGGCATGGGCTCGCTGGATGCCATGGAGAGAGCAGCAGCACCCAGAAATGATACTTCAGCGAGGGGGATA
AGGTGAAGATCACGCAGGGTGTCTCGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCGTGCCCTACCTCATAGCG
GGCATCCAGCACGGCTACCAGGATATCGGGGCCCACAGCCTGTCTGTCTTTGGGTCCATGATGTACTCAGGAGAGCTCAG
GTTTGAGAAGTGGACCATGTTGGCTCAGATCAAGCGTGGTGTCCATGGCCTGCACTCTTAGGAGAAGTGGCTGTAC

Alignment

ORF - retro_nleu_2188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 83.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGI
          IGFIHHNCTPEFQAN.V.KVKK.EQGFI.DPVVLSP...V.DV.EAK..HGF.GIP.T.TG..GS.LVGI
Retrocopy IGFIHHNCTPEFQANKVQKVKKFEQGFIMDPVVLSPSHTVGDVLEAKMPHGFSGIPTTETGTIGSKLVGI

Parental  ISSRDIDFLKEEEHDCFLEEIMTKREDLVVAPAGITLKE-ANEILQRSKKGKLPIVNEDDELVAIIARTD
          ....DIDFL.E......L.E.MT.R..LVVAPAG.TLKE.ANEILQ.SKKGKLP.VN...ELVAII.RTD
Retrocopy VTFQDIDFLAEKD-TTLLSEMMTPRTELVVAPAGVTLKE<ANEILQPSKKGKLPVVNDHGELVAIITRTD

Parental  LKKNRDYPLASKDTKKQLLCGAAIGTHEDDKYRLDLLAQAGVDVVVLDSSQGNSIFQINMIKYIKEKYPN
          LKK.RDYPLASKD..KQLLCGA..GT.EDDK.RLDLL.QAG.DV.VLDSSQGN...QI.M..YIK.KY..
Retrocopy LKKYRDYPLASKDSHKQLLCGAVVGTREDDKFRLDLLTQAGIDVIVLDSSQGNLVYQIAMVHYIKQKYLH

Parental  LQVIGGNVVTAAQAKNLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGG
          LQVIGGNVVTAAQAKNLIDAGVD.L.VGMG.GSICITQEV..CG....TAVYKV.EYA.RFGVP.IADGG
Retrocopy LQVIGGNVVTAAQAKNLIDAGVDGLHVGMGCGSICITQEVMSCGHTHGTAVYKVAEYAWRFGVPLIADGG

Parental  IQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAMDK-HLSSQNRYFSEAD
          IQ.VGH..KALALGASTVMMGSLLA.TTEA.GEYFFSD...LKKYRGMGSLDAM.....S.Q..YFSE.D
Retrocopy IQTVGHMVKALALGASTVMMGSLLATTTEASGEYFFSDRVWLKKYRGMGSLDAMER<SSSTQK*YFSEGD

Parental  KIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHS
          K.K..QGVSG..QDKGSI.KFVPYLIAGIQH..QDIGA.SL.....MMYSGEL.FEK.T..AQ...GVH.
Retrocopy KVKITQGVSGSIQDKGSIQKFVPYLIAGIQHGYQDIGAHSLSVFGSMMYSGELRFEKWTMLAQIKRGVHG

Parental  LHSYEKRLF
          LHS.EK.L.
Retrocopy LHS*EKWLY

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_2188 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,