RetrogeneDB ID: retro_ptro_2719

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:122071595..122073129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSPTRG00000019660
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:H2QVB7]

Sequence

>retro_ptro_2719
AGCCTGACGGACTACCTGATGAGCCGGGGCACCGGCTGCGTGCCCGAGGACGGGCTCACCACGCAGCAGCTCTTCGCCAG
AGCCGACAGCCTCACCTACAACGAGTTCCTGATTCTCCCAGGATTTATAGACTTCATAGCTGATGAGGCGGACCTGACCT
CAACCCTTACCTGGAAGATCACGCTGAAGACGCCGCTGATCTCTTCCTCCATGGACACTGTGACAGAGGGCAACATGGCC
ATCACGATGGCTCTGGTGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGCCAAGGAGGTGCGGAA
GGTCAAGAAGTTTGAACATGGCTTCATCACGGACCCCATGGTGCTGAGCCCCTCGCACCCTGTGGGTGATGTGCTGGAGG
CCACGATGCGGCATGGCTTCTCTGGTATCCCCATCACTGAGACAGGCACCATGGGCAGCAAGCCGGTGGGCATTGTCACC
TCCTGAGACATCGACTTTCTTGCTGAGAAGGACCACACCACCCTCCTCAGTGAGGTGATGATGCCAAGGATTGAGCTGGT
GGTGGCTCCAGCAGGAGTGATGTTGAAAGAGGCAAATGAGATCCTGCAGCAAAGCAAGAAAGTGAAGCTGCCTATCGTCA
ATGATGACGATGAGCTGGTGGCCATCATTGCCCTCACCGACCTGAAGAACCGAGACTACCCTGTGGCCTCCAAGGATTCC
CATGAGCAGCTGCTGTGTGGGGCAGCTGTGGGCACCTGTGAGGATGACAAATACCACCTGGATCTGCTCACCCAGGCGGG
TGTCGACGTCATAGTCTTGGACTTGTCCGAAGGGAACTTGCTGTATCAACTGCCATGGTGTATTACATCAAACAGAAGTA
CTCCCACCTCCAGGTGATTGGGGGGAACGTGGTGACAGCAGCCCAGGCCAAGAACCTGACTGACGCTGGTGTGGACGGGC
TGTGTGTGGGCATACGCTGCGGCTCCCTCTGCATCACCCCGGAAGTGATGGCATGTGGTTGCCCCCAGGACACTGTGTGT
ACAAGGTGGCTGAGTATGCCCAGCACTTTGGTGTGCCCATCATAGCCGATGGTGGCATCCTGACTGTGGGGCACGTCAAG
GTGCTGGCCCTTGGTGCCTCCATAGTGATGATGGGCTCGCTGCTGGCTGCCACCTTGGAGGCCCCCAGCGAATAGTTCTC
AGATGGGGTGCGGCTCAAGAAATACTGGGGCACAGGCTTGCTGGATGCCATAGAGAAGAGCAGCAGCAGCCAGGAACGAT
ACTTCAGTGAGGGGGATAAAGTGAAGATCACACAGGGTGTCTCGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTC
GTGCCCTACCTCACAGTGGGCATCCAGCATGGCTGCCAGGATATCAGGGCCCGCAGCCTGTCTGTCCTTTGGTCCATGAT
GTACTCAGGAGAGCTCAAGTTTGAGAAGCGTACCATGTTGGCCCAGATTGAGGGTGGCGTCCATGGCCTGCACTCTTAGG
AGAAGCGGCTGTAC

Alignment

ORF - retro_ptro_2719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.3 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSP
          S..DYL.S.GTG.VPEDGLT.QQLFA.AD.LTYN.FLILPGFIDFIADE.DLTS.LT.KITLKTPLISS.
Retrocopy SLTDYLMSRGTGCVPEDGLTTQQLFARADSLTYNEFLILPGFIDFIADEADLTSTLTWKITLKTPLISSS

Parental  MDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGF
          MDTVTE..MAI.MAL.GGIGFIHHNCTPEFQA.EVRKVKKFE.GFITDP.VLSPSH.VGDVLEA.MRHGF
Retrocopy MDTVTEGNMAITMALVGGIGFIHHNCTPEFQAKEVRKVKKFEHGFITDPMVLSPSHPVGDVLEATMRHGF

Parental  SGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKL
          SGIPITETGTMGSK.VGIVTS.DIDFLAEKDHTTLLSEVM.PRIELVVAPAGV.LKEANEILQ.SKK.KL
Retrocopy SGIPITETGTMGSKPVGIVTS*DIDFLAEKDHTTLLSEVMMPRIELVVAPAGVMLKEANEILQQSKKVKL

Parental  PIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGN
          PIVND.DELVAIIA.TDL.KNRDYP.ASKDS..QLLCGAAVGT.EDDKY.LDLLTQAGVDVIVLD.S.GN
Retrocopy PIVNDDDELVAIIALTDL-KNRDYPVASKDSHEQLLCGAAVGTCEDDKYHLDLLTQAGVDVIVLDLSEGN

Parental  SVYQI-AMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQ-GTAV
          ..YQ..AMV.YIKQKY.HLQVIGGNVVTAAQAKNL.DAGVDGL.VG..CGS.CIT.EVMACG.PQ.G..V
Retrocopy LLYQL<AMVYYIKQKYSHLQVIGGNVVTAAQAKNLTDAGVDGLCVGIRCGSLCITPEVMACGCPQ<GHCV

Parental  YKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSL
          YKVAEYA..FGVPIIADGGI.TVGH.VK.LALGAS.VMMGSLLAAT.EAP.E..FSDGVRLKKY.G.G.L
Retrocopy YKVAEYAQHFGVPIIADGGILTVGH-VKVLALGASIVMMGSLLAATLEAPSE-*FSDGVRLKKYWGTGLL

Parental  DAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGE
          DA.EKSSSSQ.RYFSEGDKVKI.QGVSGSIQDKGSIQKFVPYL..GIQHGCQDI.ARSLSVL.SMMYSGE
Retrocopy DAIEKSSSSQERYFSEGDKVKITQGVSGSIQDKGSIQKFVPYLTVGIQHGCQDIRARSLSVLWSMMYSGE

Parental  LKFEKRTMSAQIEGGVHGLHSYEKRLY
          LKFEKRTM.AQIEGGVHGLHS.EKRLY
Retrocopy LKFEKRTMLAQIEGGVHGLHS*EKRLY

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	0.13 RPM	46.92 RPM
SRP007412_cerebellum	0.00 RPM	18.03 RPM
SRP007412_heart	0.03 RPM	6.44 RPM
SRP007412_kidney	0.10 RPM	12.74 RPM
SRP007412_liver	0.10 RPM	7.14 RPM
SRP007412_testis	0.11 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2719 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2719 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2719 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4005
Gorilla gorilla	retro_ggor_2688

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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	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	ENSPTRG00000014908	1 retrocopy	retro_ptro_501,
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,