RetrogeneDB ID: retro_nleu_2508

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397364.1:304283..305255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSNLEG00000012341
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_nleu_2508
GGCGTGACGTTGAAAGAGGCAAATGAGATCCTGCAGCATAGCAAGAAAGGGAAGCTGCCTATCGTCAGTGATCACGATGA
GCTGGTGGCCATCATTGCCCACACTGACCTGAAGAAGAATCGAGACTACCCTCTGGCCTCCAAGGATTCCCACAAACAGC
TGTTGTGCGGGGCAGCTGTAGACATCCATGAGGATGACAAATACCACCTGGACCTGCTCACCCAGGTGGGCGTCAACGTC
ATAGTCTTGGATTCGTCCCAAGGGAACTCGGTGTATCAGATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCT
CCAGGTGATTGGGGGGGAACGTGGTGGCAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGGACGGGCTGCATGTG
GGCATGGGCTACAGCTCCATCTGCATCACCCAGGAAGTGATGGCCTCCAGTTTGCCCCAGGGCACTGCTGTGTACAAGGT
GGCCAAGTATGCCCAGTGCTTTGGTGTGCCCATCATAGTCGATGGCGGCATCCAGACCTTGGGGCACGTGGTCAAGGCCC
TGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCTGCTGGCCACCACCATGGAGGCACCCGGTGAGTACTTCTTCTTAG
AAAGGGTGCAACTCAAGAAGTACCAGGGCATGGGCTCACTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAAACAATAC
TTCAGCGAGGGGGATAAGGTGAAGATCACACAGGGTGTCTCGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCAT
GCCCTATCTCATAGCGGGCATCCAGCACAGCTGCCAGGTTATCGGGGCCCACAGCCTTTCTGTCCTTTGGTCCATGATGT
ACTCAGGGGAGCTCAAGTTTGAGAAGCGGACCATATCGGCCCAGATCAAGGGTGGTGTCCATGGCCTGCACTCTTACGAG
AAGCAGCTGTAC

Alignment

ORF - retro_nleu_2508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 55.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVTLKEANEILQRSKKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRL
          GVTLKEANEILQ.SKKGKLPIV.D.DELVAIIA.TDLKKNRDYPLASKDS.KQLLCGAAV...EDDKY.L
Retrocopy GVTLKEANEILQHSKKGKLPIVSDHDELVAIIAHTDLKKNRDYPLASKDSHKQLLCGAAVDIHEDDKYHL

Parental  DLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGG-NVVTAAQAKNLIDAGVDGLRVGMGCGS
          DLLTQ.GV.VIVLDSSQGNSVYQI.MVHYIKQKYPHLQVIGG.NVV.AAQAKNLIDAGVDGL.VGMG..S
Retrocopy DLLTQVGVNVIVLDSSQGNSVYQITMVHYIKQKYPHLQVIGG>NVVAAAQAKNLIDAGVDGLHVGMGYSS

Parental  ICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGS-LLAATTEAPG
          ICITQEVMA...PQGTAVYKVA.YA..FGVPII.DGGIQT.GHVVKALALGASTVMMGS.LLA.T.EAPG
Retrocopy ICITQEVMASSLPQGTAVYKVAKYAQCFGVPIIVDGGIQTLGHVVKALALGASTVMMGS<LLATTMEAPG

Parental  EYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGC
          EYFF...V.LKKY.GMGSLDAMEKSSSSQK.YFSEGDKVKI.QGVSGSIQDKGSIQKF.PYLIAGIQH.C
Retrocopy EYFFLERVQLKKYQGMGSLDAMEKSSSSQKQYFSEGDKVKITQGVSGSIQDKGSIQKFMPYLIAGIQHSC

Parental  QDIGARSLSVLRSMMYSGELKFEKRTMSAQIEGGVHGLHSYEKRLY
          Q.IGA.SLSVL.SMMYSGELKFEKRT.SAQI.GGVHGLHSYEK.LY
Retrocopy QVIGAHSLSVLWSMMYSGELKFEKRTISAQIKGGVHGLHSYEKQLY

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_2508 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 9 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017770	1 retrocopy	retro_cjac_2045,
Homo sapiens	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
Gorilla gorilla	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798, retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
Macropus eugenii	ENSMEUG00000016082	2 retrocopies	retro_meug_2095, retro_meug_542,
Macaca mulatta	ENSMMUG00000014509	2 retrocopies	retro_mmul_1551, retro_mmul_317,
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	ENSPPYG00000017976	7 retrocopies	retro_pabe_2133, retro_pabe_2138, retro_pabe_2346, retro_pabe_3102, retro_pabe_3292, retro_pabe_3392, retro_pabe_3736,
Pan troglodytes	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,