RetrogeneDB ID: retro_pabe_3392

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:27481440..27482958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSPPYG00000017976
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_pabe_3392
AGCGTGGTGGACTACCTGATCAGCGGTGGCACTGGCTACATGCCCGAGGACGGGCTCATCGCACAGCAGCTCTTCGCCAG
CGCCTAAGGCCTCACCTAGGACGACTTCCTGATTCTCCCAGGACTCATAGACTTCATAGCTGAGGTGGACCTGACCTCAG
CCCTGACCCGGAAGATCACGCTGAAGACACCGCTGATCTCCTCCCCCATGGACACTGTGACAGAGGCTGACATGGCCATC
GCGATGGCTCTGATGGGAGATATTGGTTTCATTCACCACAACTGCACCCCAGAGCTCCAGGCCAAGGAGCTAGGGAAGGT
CAAGAAGTTTGAGCAGGGCTTCATCACGGACCCCATGGTGCTGAGCCCCTCCCACACTGTAGGTGATGTGCTGGAGGCCA
AGATGCGGCATGGCTTCTCTGGCACCCCCATCACTGAGACGGGCACCATGGGCAGCAAGCTGGCGGGCATCGTCACCTCC
TGAGACATCAACTTTCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGAGGTGATGACACCAAGGCTCGAGCTGGTGGT
GGCTCCAGCATGTGTGACGTTGAAAGAGGCAAATGAGATCCTGCAGCGTAGCAAGAAAGGGAAGCTGCCTATCATCAATG
ATCGCAATGAGCTGGTGGCCATTATCACCAGCAGCGACCTGAAGAAGAACCAAGACTACCCTCTGGCCTCCAAGGATTCC
CACAAGCAGCTGCTGTGCGGGGCAGCTGTGGGCACCCGTGAGGATGACAAATATCGCCTGGACCTGCTCACCCAGATGGG
CGTCGACATCATAGTCTTGGACTCGTCCCGAGGGAACTTGGTGTATCAGATCGCCATGGTGCATTATATCAAACAGAAGT
ACCCCCACCTCCAGGTGATTGGCAGGAACGTGGTGACAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGCACGGG
CTGTGCATGGGCATGGGCTGCGGCTCCATCTGCGTCACCTGGGAAGTGATGGCTTGTGGTCAGCCCCAGGGCACTGCTGT
GTACAAGGTGGCCGAGTATGCCCGGCGCTTTGGTGTGCCCATCATAGCCAATGGCGGCATCCAGACTGTGGGGCACATAG
TCAAGGCCCTGGCCCTTGGAGTCTCCACAGTGATGATGAGCTCCCTGCTGGCCACCACCACGGAGGCCCCTGGTGAGTAC
TTCTCAGACGAGGTGCAGCTCAAGAAGTACCGGGGCATGAGCTCGCTGGATGCCATGGAGAAGAGCAGCAGCAGCCAGAA
ACGATACTTCAGCAAGGGGGGTAAGGTGAAGATCGCGCACGGTGTCTTGGGCTCCATCCAGGACAAAGGGTCCATTCAGA
AGTTCGTGCCCTACCTCATAGTGGGCATCCAGCACGGCTGCCAGGATATCGGGGCCCACAGCCTGTCTGTCCCTCGGTCC
ATGATGTACTCAGGAGAGCTCAAGTTTGAGAAGGGGATCATGTCGGCCCAGATCGAGGGTGGCGTCCATGGTCTGCAC

Alignment

ORF - retro_pabe_3392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 85.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMADYLISGGTGYVPEDGLTEQKNFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSP
          S..DYLISGGTGY.PEDGL..Q..FASA.GLT..DFLILPG.IDFIA.EVDLTSALTRKITLKTPLISSP
Retrocopy SVVDYLISGGTGYMPEDGLIAQQLFASA*GLT*DDFLILPGLIDFIA-EVDLTSALTRKITLKTPLISSP

Parental  MDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGF
          MDTVTEADMAIAMALMG.IGFIHHNCTPE.QA.E..KVKKFEQGFITDP.VLSPSHTVGDVLEAKMRHGF
Retrocopy MDTVTEADMAIAMALMGDIGFIHHNCTPELQAKELGKVKKFEQGFITDPMVLSPSHTVGDVLEAKMRHGF

Parental  SGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKL
          SG.PITETGTMGSKL.GIVTS.DI.FLAEKDHTTLLSEVMTPR.ELVVAPA.VTLKEANEILQRSKKGKL
Retrocopy SGTPITETGTMGSKLAGIVTS*DINFLAEKDHTTLLSEVMTPRLELVVAPACVTLKEANEILQRSKKGKL

Parental  PIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGN
          PI.NDR.ELVAII...DLKKN.DYPLASKDS.KQLLCGAAVGTREDDKYRLDLLTQ.GVD.IVLDSS.GN
Retrocopy PIINDRNELVAIITSSDLKKNQDYPLASKDSHKQLLCGAAVGTREDDKYRLDLLTQMGVDIIVLDSSRGN

Parental  SVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYK
          .VYQIAMVHYIKQKYPHLQVIG.NVVTAAQAKNLIDAGV.GL..GMGCGSIC.T.EVMACG.PQGTAVYK
Retrocopy LVYQIAMVHYIKQKYPHLQVIGRNVVTAAQAKNLIDAGVHGLCMGMGCGSICVTWEVMACGQPQGTAVYK

Parental  VAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDA
          VAEYARRFGVPIIA.GGIQTVGH.VKALALG.STVMM.SLLA.TTEAPGEY.FSD.V.LKKYRGM.SLDA
Retrocopy VAEYARRFGVPIIANGGIQTVGHIVKALALGVSTVMMSSLLATTTEAPGEY-FSDEVQLKKYRGMSSLDA

Parental  MEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGELK
          MEKSSSSQKRYFS.G.KVKIA.GV.GSIQDKGSIQKFVPYLI.GIQHGCQDIGA.SLSV.RSMMYSGELK
Retrocopy MEKSSSSQKRYFSKGGKVKIAHGVLGSIQDKGSIQKFVPYLIVGIQHGCQDIGAHSLSVPRSMMYSGELK

Parental  FEKRTMSAQIEGGVHGLH
          FEK..MSAQIEGGVHGLH
Retrocopy FEKGIMSAQIEGGVHGLH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	16.92 RPM
SRP007412_cerebellum	0.12 RPM	9.12 RPM
SRP007412_heart	0.03 RPM	3.31 RPM
SRP007412_kidney	0.07 RPM	8.88 RPM
SRP007412_liver	0.00 RPM	5.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3392 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3392 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4247
Pan troglodytes	retro_ptro_2886

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 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	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
Pongo abelii	ENSPPYG00000013884	1 retrocopy	retro_pabe_528,
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,