RetrogeneDB ID: retro_ptro_1087

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:10257689..10259090(+)
• 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_1087
AGCATGGTTGACCATCTGATCAGTGGCAGCACCGGCTACGTGCCCCAGGACTGGCTCACCATGCAGCAGTCTTCCTCAGC
GCGAACTGCCTCACCCACAACAACTTCCTGATTCTCCCATGGTTCATAGATTTCATAGCTGATGAGGTAGACCTAACTTC
AGCCCTGACCCGGAAGATCATGCTGAAGACACCGCTGATCTCCTCCCCTATGGACACTGAGACAGAGGCCGACATGGCCA
TCGCGATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGCCAACGAGGTGCATAAG
GTCAAGAAGTTTGAACAGGGCTTCATCACGGACCCCGTGGTGCTGAGCCCCTCACACACTGTGGGTGATGTGCTGGAGGC
CAAGATCCGGCATGGCTTCTCTTGCATCCCCATCACTGAGATGGGCACCACGGGCAGCAAGTTGGTGGGCATCATCTCCT
CCCGAGACATCGACTTTCTTGCTGAAAAGGACCACACCACCCTCCTCAGTGAGGTGATGACGCCAAGGATCGAGCTGATG
GTGGCTCCAGCAGACATGACATTGAAAGAGGCAAATGAGATCCTTTAGCCTAGCAAGAAAGGGAAGCTGCCTATGGTCAA
TGATCGCCATGAGCTAGTGGCCATCATCGCCCACACCAACCTGAAGAAGAATCGAGACTACACTCTGGCCTCCAAGGATT
CCCACAAGCAGCTCTGTGCAGGGTAGCTGTGGGCACCCGTGAGGATGACAAATACTGCCTGGGCCTGCTCACCTGGGTAG
GCATCAATGTCATAGTCTTGGACTCCTCCCAAGGAACTCAGTGTATCAAATCACCATGGTGCATTACATCAAACAGAAGT
ACCCCCACCTCCAGGTGACTGGGAGGAATGTGGTGACAGCAGCCCAGGCCGAGAACCTGACTGACACTGGTGTGGAGGGA
CTGCACGTAGGTATGGGCTGCAGCTCTATCTGCATCACCCAGGAAGTGATGGCCTGTGGTCAGCCCCAGGGCACTGCTGT
GTACAAGGTGGCCAAGTATGCTCAGCACTTTGGTGTGTCCATCATAGCCGATGTGGCATCCAGACCGTGGGGCACGTGGT
CAAGGCCCTGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCCTGCTGGCCACCACCACGGAGGCCCACTGGCGAGTAC
TTCTTCTCAGACAGGGTGCGGCTCAAGAAGTACCAGGGCATGGGCTCGCTAGATGCCATGGAGAAGAGCAGCAGCAGCCA
GAAACGATACTTCAGTGAGGGGGAAAAGGTGAAGATTGTGCAGGGTGTCTGGGCCTCCATCCAGGACAAAGGGTCCATTC
AGAAGTTTGTGCCCTACCTCATAGCGAGTATCCAGCATGGC

Alignment

ORF - retro_ptro_1087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.2 %
• Parental protein coverage: 78.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SMADYLISGGTGYVPEDGLTAQQ-LFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISS
          SM.D.LISG.TGYVP.D.LT.QQ..F.SA..LT.N.FLILP.FIDFIADEVDLTSALTRKI.LKTPLISS
Retrocopy SMVDHLISGSTGYVPQDWLTMQQ<VFLSANCLTHNNFLILPWFIDFIADEVDLTSALTRKIMLKTPLISS

Parental  PMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHG
          PMDT.TEADMAIAMALMGGIGFIHHNCTPEFQANEV.KVKKFEQGFITDPVVLSPSHTVGDVLEAK.RHG
Retrocopy PMDTETEADMAIAMALMGGIGFIHHNCTPEFQANEVHKVKKFEQGFITDPVVLSPSHTVGDVLEAKIRHG

Parental  FSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGK
          FS.IPITE.GT.GSKLVGI..SRDIDFLAEKDHTTLLSEVMTPRIEL.VAPA..TLKEANEIL..SKKGK
Retrocopy FSCIPITEMGTTGSKLVGIISSRDIDFLAEKDHTTLLSEVMTPRIELMVAPADMTLKEANEIL*PSKKGK

Parental  LPIVNDRDELVAIIARTDLKKNRDYPLASKDSQKQL-LCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQ
          LP.VNDR.ELVAIIA.T.LKKNRDY.LASKDS.KQL.LC..AVGTREDDKY.L.LLT..G..VIVLDSSQ
Retrocopy LPMVNDRHELVAIIAHTNLKKNRDYTLASKDSHKQL<LCRVAVGTREDDKYCLGLLTWVGINVIVLDSSQ

Parental  G-NSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTA
          G.NSVYQI.MVHYIKQKYPHLQV.G.NVVTAAQA.NL.D.GV.GL.VGMGC.SICITQEVMACG.PQGTA
Retrocopy G<NSVYQITMVHYIKQKYPHLQVTGRNVVTAAQAENLTDTGVEGLHVGMGCSSICITQEVMACGQPQGTA

Parental  VYKVAEYARRFGVPIIAD-GGIQTVGHVVKALALGASTVMMGSLLAATTEA-PGEYFFSDGVRLKKYRGM
          VYKVA.YA..FGV.IIAD..GIQTVGHVVKALALGASTVMMGSLLA.TTEA..GEYFFSD.VRLKKY.GM
Retrocopy VYKVAKYAQHFGVSIIAD<CGIQTVGHVVKALALGASTVMMGSLLATTTEA>TGEYFFSDRVRLKKYQGM

Parental  GSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHG
          GSLDAMEKSSSSQKRYFSEG.KVKI.QGV..SIQDKGSIQKFVPYLIA.IQHG
Retrocopy GSLDAMEKSSSSQKRYFSEGEKVKIVQGVWASIQDKGSIQKFVPYLIASIQHG

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	0.32 RPM	46.92 RPM
SRP007412_cerebellum	0.14 RPM	18.03 RPM
SRP007412_heart	0.00 RPM	6.44 RPM
SRP007412_kidney	0.00 RPM	12.74 RPM
SRP007412_liver	0.00 RPM	7.14 RPM
SRP007412_testis	0.00 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1087 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1087 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1551

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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,