Gene loci information

Transcript annotation

  • This transcript has been annotated as Trifunctional purine biosynthetic protein adenosine-3.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11988 g11988.t1 TSS g11988.t1 20147282 20147282
chr_1 g11988 g11988.t1 isoform g11988.t1 20147416 20151772
chr_1 g11988 g11988.t1 exon g11988.t1.exon1 20147416 20147452
chr_1 g11988 g11988.t1 cds g11988.t1.CDS1 20147416 20147452
chr_1 g11988 g11988.t1 exon g11988.t1.exon2 20147513 20147655
chr_1 g11988 g11988.t1 cds g11988.t1.CDS2 20147513 20147655
chr_1 g11988 g11988.t1 exon g11988.t1.exon3 20147774 20148894
chr_1 g11988 g11988.t1 cds g11988.t1.CDS3 20147774 20148894
chr_1 g11988 g11988.t1 exon g11988.t1.exon4 20148958 20151772
chr_1 g11988 g11988.t1 cds g11988.t1.CDS4 20148958 20151772
chr_1 g11988 g11988.t1 TTS g11988.t1 20151849 20151849

Sequences

>g11988.t1 Gene=g11988 Length=4116
ATGGAGAAGAAGAATGTTTTGTTAATTGGAAGTGGAGGACGTGAGCACGCATTAGCTTGG
AAACTTCAACAGAGCAAACATGTAGCTCATATTTTTACATTTCCTGGATCATTTGCCATA
TCGCAGCTTGAAAAAGCAAAGATAGTGAGCAGCAATGAGATGAATCTCAAAGATTTCACG
GGGATAGCTGCATGGTGCAAAAACAATATTATTGATCTTGTCGTTGTTGGGCCAGAAGAT
CCTCTTGCTGAGGGAATCGCCGATGTTCTCAAGAAAAATGGCATACCATGCTTTGGACCA
TCAAAAGCAGGTGCGAGAATTGAATCTGACAAGAGTTGGTCAAAGGAATTCATGATTAAA
CATAACATTCCGACTGCACGCTATGGATCTTTTACTGATGCAAATAAAGCAAAAGAATAC
ATTAAAAATACAAGAAATGCACTCGTGGTCAAAGCGAGTGGACTAGCTGCTGGAAAAGGA
GTTATCGTTGCAGAAACAATTGACGAGGCATGTGCAGCTGTTGATGAAATATTAGGAGAT
CATAAATTTGGATCAGCTGGAGATGTAGTTGTTGTTGAAGAAAAACTTTCTGGTCAAGAA
ATTTCCGTTTTGGCATTTGTTGATTCTAATTCCGTAAGATTGCTATTGCCAGCACAAGAT
CACAAACGTTTATTAGATAACGATGAAGGTCTTAATACTGGCGGAATGGGTGCTTATTGT
CCATGTCCATTGATTAGTCAGCAAGAATTAGATATTGTTAAAACACAAGTTTTACAGCGT
GCTGTCGATGGATTACGTGTTGAAGGCATATCGTATAATGGAATTTTATATGCAGGAATG
ATGCTCACTCCTGATGGACCTAAAACTTTAGAATTCAATTGTCGTTTTGGCGATCCTGAA
ACTCAAGTTATTTTGCCACTCTTAGAAAATGATTTGTTTGATTTAATGACTGCAACATGC
TCGAATCAACTCTGTAATGTACCAGAATTAGAATTCAAATCAAATATAAATGCTGTTGGT
GTTGTAATGGCATCAAAAGGATATCCGCAAACATCAACCAAGGGTTGTGTAATTGAAGGT
ATTGAACAAGTCAATGCTAAAGAAAATCACATTGTTTTCCATAGTGGAACAACTAAAAAT
GATAAAAATCAATGGGTTACAAACGGTGGCCGTGTTCTTATTAATGTTGCTTTAGCAAAT
GATTTAAAATCAGCAGCAGATTTAGCAACACAAGCTTCTGACGTTATTAAATTTGAAGGA
GCTCAATATCGTCGTGATATTGCAAAGAAAGCAATAAAAATACAACCAATTTCATATAAA
AACAGTGGTGTGGATATAGAAGCTGGTGAATCTCTAGTACAAAGAATCAAGCCGCTTGCT
CGAGGAACAAATCGAAGTGGCGTTATTGGTGAAATAGGCAGCTTTGGTGGATTAATCAAA
TTAAACGACATTAAATATATCGATAAAAATGGTTTGGAGACAAATTATAAAGATCCTGTT
TTAGTTCAGGGAACAGATGGGGTAGGAACTAAATTGAAAATTGCAGAAGCACTCAATATT
TGGGATACAATTGGAATTGATCTTGTCGCTATGTGTGTCAACGATGTATTATGTAATGGA
GCAGAACCTGTTGCATTTCTCGATTATATAGCTTGTGGCCTCCTCGATGTTCCATCTGCT
GCAATGATTGTTAAAGGAATATCAGAAGCATGTCGTGAATCAAATTGTGCACTAATAGGT
GGTGAAACTGCAGAAATGCCTTCCATGTATGAAAAAGGAAAATATGATTTGGCAGGTTAT
TGCGTCGGAATTGTTGAATATGAAGATATTTTACCTAAAATGAATGAAGTTCGTGAAGGT
GATATTGTTGTTGCTTTACCATCAAGTGGTATTCATAGCAATGGTTTCTCACTTGTCAAT
AAAATTCTTGAAAAATTGGATTTTAAATTGACTGATATTGCACCATTCAGTGATGATGGC
AACTCATTTGGAAAAGAATTTTTGACACCAACAAAATTATATGTTTCTAATGTAATGCCA
TTGTTGAGAAAAGGAAATGTTAAATCACTTGCTCACATTACAGGTGGAGGATTATATGAA
AATATTCCAAGAGCTCTACCATCAAATGTTTGTGTACAACTCGATGCAGTTACATGGAAG
TTACCAAAAGTGTTTGGTTGGTTAGCAGCACAAGGCAATATTGATGAAAATGAAATGCTA
AGAACTTTTAATTGTGGCATTGGAATGATCATTATTTTACCACGAAATAATATTGAATGG
CAGTCGATTTCAGAAGCAAAATTGATTGGAAATGTTACAAAACGAGAAACATCAGATTCA
CCACAAGTAATTGTGAAAAATTTCAAAGAAGTGCTCGAAAAAGAAATTTCACCATGGAAA
AATGCATCAAACTCTACCACAATCAGTTATAAAGATAGTGGTGTGGATATTATTGCTGGA
AATGCTCTTGTCGATAATATCAAGCCCTTTGCAAAATCAACCAATCGCAAAGGAGTTCTA
GGTGGTCTTGGTTCTTTTGGAGGTTTATTTAGATTAAAAGAACTTGAGCAAGTTTACACT
GATCCTGTGCTGGTTCTTTCTACAGACGGTGTAGGAACAAAATTGAAAATTGCTCAACAA
ATTGGAAAGCATGACACAATTGGAATAGATTTAGTTGCTATGTGTAATAATGACATTTTA
TGCAATGGAGCAGAACCTCTCACATTTTTAGATTATTATGCATGCGGTAAACTTGACGTA
AACACAGCAACAAGTGTTATTTCTGGCATTTCAAAAGGATGTGAACAAAGCAATTGTGCA
TTATTAGGTGGTGAAACTGCAGAAATGCCTGGAGTATATATGCCAAATGTTTATGATCTT
GCTGGTTTCGCTCTTGGTATCACTGAATTTTCTGAAACACTTCCAAAAATAAATGCAATC
GAGGAAGGTGACATTGTAATTGGGTTTCCTTCTCAAGGTGTGCATAGTAATGGCTTTAGT
TTAATTCATAAACTACTTGATTTAACTGGACATAAATGGAATGATATTGCACCATTTAGT
GCTAATAGCAAAACATTTGGTGAAGAATTTTTGGAACCAACTAAAATTTATGTTAAGGAA
GTTTTACCAGCTATCAAAACTGGTTATGTTAAAGCTCTCGCTCACATAACTGGTGGAGGT
TTATGGGAAAATATTCCAAGAGTTCTTTCATATAATCTCACAGCTGAACTTAATGCAAAG
TTGTTCAATATTCCTCCAGTTTTTGCATGGCTTTCTTTATGTGGAAATATTGACAAACTG
GAATTAATGAAGACATTTAATTGTGGTATTGGGATGATAATGATTGCCTCAAAAAAACAT
GAGCTTGAACTTCTTAAAATTCTTTATGGAACAAAGGCATCAGTTATTGGAAAAATCATA
AAGAGAAAAGTTAATGGTCATCAAGTAATTATTAGACATTTTAAAGAATGTTTCGAACGT
GTTGAACGGCTTTTGAGTGTTCCAAAGAAAAGAGTTGCTGTATTAATCTCAGGTAGTGGG
TCAAATTTGCAAGCTCTAATTGATGCAACGAAAAATTCAACTATGGGAATGTGTGCTGAA
ATTGTCTTTGTTTTATCAAATAAACCTGATGTATTTGGTTTAGAAAGAGCAAAAAAAGCA
AAAATTCCTTCAGCTGTTATAAGTCACAAAGATTTTCCAACAAGAGAAAAGTTTGATGAT
GCAATGCATGAAGAGCTTTTACGTCACAATGTTGATATAGTTTGTCTTGCTGGTTTTATG
AGAATTGTTACAGCAGCATTTGTCAATAAATGGAAAGGACGCTTATTAAATATACATCCA
AGTTTGCTGCCAAAATACAAAGGAATACATGCACAAAAAGATGCTTTAGAATCAGGCGAT
AAAGAGACTGGATGCACAGTTCATTTTGTTGATGAAAATGTTGATACAGGTGCCATAATT
GTACAAGAAATCGTGCCAATTTATGAAAATGATTCAGTTGAAACTTTGACTGATCGAATT
CATATAGCAGAACATGTTGCATTTCCGAAAGCCCTTCGTTTAGTAGCAAGTGGTTACGTC
TATTTATCTGACGATGGAATAACAAAATGGGCTTAA

>g11988.t1 Gene=g11988 Length=1371
MEKKNVLLIGSGGREHALAWKLQQSKHVAHIFTFPGSFAISQLEKAKIVSSNEMNLKDFT
GIAAWCKNNIIDLVVVGPEDPLAEGIADVLKKNGIPCFGPSKAGARIESDKSWSKEFMIK
HNIPTARYGSFTDANKAKEYIKNTRNALVVKASGLAAGKGVIVAETIDEACAAVDEILGD
HKFGSAGDVVVVEEKLSGQEISVLAFVDSNSVRLLLPAQDHKRLLDNDEGLNTGGMGAYC
PCPLISQQELDIVKTQVLQRAVDGLRVEGISYNGILYAGMMLTPDGPKTLEFNCRFGDPE
TQVILPLLENDLFDLMTATCSNQLCNVPELEFKSNINAVGVVMASKGYPQTSTKGCVIEG
IEQVNAKENHIVFHSGTTKNDKNQWVTNGGRVLINVALANDLKSAADLATQASDVIKFEG
AQYRRDIAKKAIKIQPISYKNSGVDIEAGESLVQRIKPLARGTNRSGVIGEIGSFGGLIK
LNDIKYIDKNGLETNYKDPVLVQGTDGVGTKLKIAEALNIWDTIGIDLVAMCVNDVLCNG
AEPVAFLDYIACGLLDVPSAAMIVKGISEACRESNCALIGGETAEMPSMYEKGKYDLAGY
CVGIVEYEDILPKMNEVREGDIVVALPSSGIHSNGFSLVNKILEKLDFKLTDIAPFSDDG
NSFGKEFLTPTKLYVSNVMPLLRKGNVKSLAHITGGGLYENIPRALPSNVCVQLDAVTWK
LPKVFGWLAAQGNIDENEMLRTFNCGIGMIIILPRNNIEWQSISEAKLIGNVTKRETSDS
PQVIVKNFKEVLEKEISPWKNASNSTTISYKDSGVDIIAGNALVDNIKPFAKSTNRKGVL
GGLGSFGGLFRLKELEQVYTDPVLVLSTDGVGTKLKIAQQIGKHDTIGIDLVAMCNNDIL
CNGAEPLTFLDYYACGKLDVNTATSVISGISKGCEQSNCALLGGETAEMPGVYMPNVYDL
AGFALGITEFSETLPKINAIEEGDIVIGFPSQGVHSNGFSLIHKLLDLTGHKWNDIAPFS
ANSKTFGEEFLEPTKIYVKEVLPAIKTGYVKALAHITGGGLWENIPRVLSYNLTAELNAK
LFNIPPVFAWLSLCGNIDKLELMKTFNCGIGMIMIASKKHELELLKILYGTKASVIGKII
KRKVNGHQVIIRHFKECFERVERLLSVPKKRVAVLISGSGSNLQALIDATKNSTMGMCAE
IVFVLSNKPDVFGLERAKKAKIPSAVISHKDFPTREKFDDAMHEELLRHNVDIVCLAGFM
RIVTAAFVNKWKGRLLNIHPSLLPKYKGIHAQKDALESGDKETGCTVHFVDENVDTGAII
VQEIVPIYENDSVETLTDRIHIAEHVAFPKALRLVASGYVYLSDDGITKWA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
34 g11988.t1 CDD cd02196 PurM 470 757 3.77477E-146
33 g11988.t1 CDD cd02196 PurM 859 1140 1.8555E-145
32 g11988.t1 CDD cd08645 FMT_core_GART 1171 1355 4.18173E-100
29 g11988.t1 Gene3D G3DSA:3.40.50.20 - 5 101 5.2E-33
27 g11988.t1 Gene3D G3DSA:3.30.1490.20 - 127 196 1.3E-25
26 g11988.t1 Gene3D G3DSA:3.30.470.20 - 197 333 2.4E-52
28 g11988.t1 Gene3D G3DSA:3.90.600.10 Glycinamide Ribonucleotide Synthetase; Chain A 337 439 1.8E-30
30 g11988.t1 Gene3D G3DSA:3.30.1330.10 - 440 611 3.3E-67
23 g11988.t1 Gene3D G3DSA:3.90.650.10 - 612 801 2.8E-65
31 g11988.t1 Gene3D G3DSA:3.30.1330.10 - 807 972 1.9E-65
24 g11988.t1 Gene3D G3DSA:3.90.650.10 - 975 1166 3.8E-63
25 g11988.t1 Gene3D G3DSA:3.40.50.170 Formyltransferase 1170 1371 1.6E-80
14 g11988.t1 Hamap MF_00138 Phosphoribosylamine–glycine ligase [purD]. 4 432 38.318745
12 g11988.t1 Hamap MF_00741 Phosphoribosylformylglycinamidine cyclo-ligase [purM]. 437 788 41.314709
11 g11988.t1 Hamap MF_00741 Phosphoribosylformylglycinamidine cyclo-ligase [purM]. 808 1151 41.377647
13 g11988.t1 Hamap MF_01930 Phosphoribosylglycinamide formyltransferase [purN]. 1171 1358 32.715412
9 g11988.t1 PANTHER PTHR10520 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED 5 790 0.0
10 g11988.t1 PANTHER PTHR10520 TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED 804 1155 0.0
2 g11988.t1 Pfam PF02844 Phosphoribosylglycinamide synthetase, N domain 5 108 1.0E-31
1 g11988.t1 Pfam PF01071 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain 110 301 7.2E-80
6 g11988.t1 Pfam PF02843 Phosphoribosylglycinamide synthetase, C domain 338 430 8.1E-26
8 g11988.t1 Pfam PF00586 AIR synthase related protein, N-terminal domain 500 605 2.8E-15
4 g11988.t1 Pfam PF02769 AIR synthase related protein, C-terminal domain 618 776 8.8E-25
7 g11988.t1 Pfam PF00586 AIR synthase related protein, N-terminal domain 864 967 3.5E-14
5 g11988.t1 Pfam PF02769 AIR synthase related protein, C-terminal domain 981 1145 2.3E-30
3 g11988.t1 Pfam PF00551 Formyl transferase 1170 1352 1.3E-65
36 g11988.t1 ProSitePatterns PS00184 Phosphoribosylglycinamide synthetase signature. 295 302 -
35 g11988.t1 ProSitePatterns PS00373 Phosphoribosylglycinamide formyltransferase active site. 1304 1327 -
43 g11988.t1 ProSiteProfiles PS50975 ATP-grasp fold profile. 115 321 32.991
38 g11988.t1 SMART SM01209 GARS_A_3 109 301 4.5E-121
37 g11988.t1 SMART SM01210 GARS_C_2 337 432 2.0E-42
16 g11988.t1 SUPERFAMILY SSF52440 PreATP-grasp domain 4 109 4.03E-30
22 g11988.t1 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 110 325 1.68E-56
17 g11988.t1 SUPERFAMILY SSF51246 Rudiment single hybrid motif 338 432 1.02E-25
20 g11988.t1 SUPERFAMILY SSF55326 PurM N-terminal domain-like 437 610 5.68E-44
19 g11988.t1 SUPERFAMILY SSF56042 PurM C-terminal domain-like 615 776 4.36E-49
21 g11988.t1 SUPERFAMILY SSF55326 PurM N-terminal domain-like 807 969 6.43E-45
18 g11988.t1 SUPERFAMILY SSF56042 PurM C-terminal domain-like 979 1143 1.64E-49
15 g11988.t1 SUPERFAMILY SSF53328 Formyltransferase 1170 1368 7.46E-64
39 g11988.t1 TIGRFAM TIGR00877 purD: phosphoribosylamine–glycine ligase 5 432 1.0E-152
40 g11988.t1 TIGRFAM TIGR00878 purM: phosphoribosylformylglycinamidine cyclo-ligase 437 760 9.0E-121
41 g11988.t1 TIGRFAM TIGR00878 purM: phosphoribosylformylglycinamidine cyclo-ligase 808 1141 1.1E-120
42 g11988.t1 TIGRFAM TIGR00639 PurN: phosphoribosylglycinamide formyltransferase 1170 1358 8.9E-78

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0009113 purine nucleobase biosynthetic process BP
GO:0006189 ‘de novo’ IMP biosynthetic process BP
GO:0046872 metal ion binding MF
GO:0009058 biosynthetic process BP
GO:0004641 phosphoribosylformylglycinamidine cyclo-ligase activity MF
GO:0016742 hydroxymethyl-, formyl- and related transferase activity MF
GO:0004637 phosphoribosylamine-glycine ligase activity MF
GO:0004644 phosphoribosylglycinamide formyltransferase activity MF

KEGG

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values