Gene loci information

Transcript annotation

  • This transcript has been annotated as CAD protein.

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 g13252 g13252.t1 isoform g13252.t1 28790271 28794792
chr_1 g13252 g13252.t1 exon g13252.t1.exon1 28790271 28790277
chr_1 g13252 g13252.t1 cds g13252.t1.CDS1 28790271 28790277
chr_1 g13252 g13252.t1 exon g13252.t1.exon2 28790441 28790496
chr_1 g13252 g13252.t1 cds g13252.t1.CDS2 28790441 28790496
chr_1 g13252 g13252.t1 exon g13252.t1.exon3 28790561 28791042
chr_1 g13252 g13252.t1 cds g13252.t1.CDS3 28790561 28791042
chr_1 g13252 g13252.t1 exon g13252.t1.exon4 28791107 28791869
chr_1 g13252 g13252.t1 cds g13252.t1.CDS4 28791107 28791869
chr_1 g13252 g13252.t1 exon g13252.t1.exon5 28791926 28793076
chr_1 g13252 g13252.t1 cds g13252.t1.CDS5 28791926 28793076
chr_1 g13252 g13252.t1 exon g13252.t1.exon6 28793137 28794033
chr_1 g13252 g13252.t1 cds g13252.t1.CDS6 28793137 28794033
chr_1 g13252 g13252.t1 exon g13252.t1.exon7 28794105 28794792
chr_1 g13252 g13252.t1 cds g13252.t1.CDS7 28794105 28794792
chr_1 g13252 g13252.t1 TSS g13252.t1 28795447 28795447
chr_1 g13252 g13252.t1 TTS g13252.t1 NA NA

Sequences

>g13252.t1 Gene=g13252 Length=4044
ATGACAAACGACGTCTGTCTAGTTCTTGAAGATGGAACAATTCTATCGGGTCAAAAATTT
GGTGCTGATAGAGATGTCGATGGTGAGGTTGTTTTTCAGACTGGAATGGTTGGTTATATT
GAATCGATGACTGATCCATCTTATCATGGACAAATTTTGGTTCTTACATATCCATTAATC
GGAAATTATGGCGTTCCTACTGAAACTGAATTTGATGAAAATCAACTGATTAAACATTTC
GAATCTGACAATAAAATTTGGATTTCTGGTTTAATTGTTGGTGAACTTTGTGATGATCCG
TCTCATTGGCGTTTAAAATACAAATTAGCTGAATGGATGAAAAAGCACAATGTAGCTGGA
ATTAGTGGAATTGATACGAGAGCTTTGACAAAGCAAATTCGTGAAAATGGAACTGTTTTA
GGAAAAATTGTTCAGCAGCCATCGGGTCCTTTTCTCGGAATTGAATTTAAAGATCAAAAT
GAACGAAATTTGGTAGCAGAAGTTTCAACAAAAGTAGCAAAGACTTACAATGCAAATGGC
TCACCTCGCATTTGTGCAGTTGATTGTGGATTGAAATTGAATCAAATTCGATGCTTCATC
AAACGTGGAGCACGTGTCGATGTTGTGCCATGGGATCATCCACTCAATCCAAAAGATTTC
GACGGTCTTTTCCTTAGCAATGGTCCAGGTGACCCTGTCATGTGTCATAAAACTGTAAAA
AATATTCAACAGGTACTTGCATCATCCAATGCAAAGCCAATTTTTGGTATTTGTTTGGGT
CATCAATTACTCTCAACTGCAATCGGCTGTAAAACTTACAAAATGAAGTACGGAAACCGT
GGACATAATTTACCTGCACTCCATCATGGCACAAATCGTTGCTTTATGACTTCACAAAAT
CATGGTTTTGCTGTTGATGCAACAACTATTGATAATGCCAATTGGGAGCCACTTTTTACG
AATTTAAACGACAACTCAAATGAAGGAATTGTACATAAAGAAAAGCCATATTTCAGTGTA
CAATTTCATCCAGAACATACTGCAGGTCCTGAAGATTTGGAATGTTTATTTGATGTATTT
TTAGATAGTGTTAAAGACAATATGAAAAATGTTACTGGTTTGTCAATCAAAAATAGACTA
TTGAAGAAACTTATTTATGTGCCAAAAGTACAACTTGAACGGCGTCCTAAAAAAGTCTTA
ATTCTTGGTTCCGGTGGTTTGTCAATTGGTCAAGCTGGAGAATTTGATTATTCTGGCTCA
CAAGCTATTAAAGCTATGCAAGAGGAGAAAATTCAGACTGTTTTAATTAATCCTAATATT
GCTACAGTTCAAACTTCAAAAGGTCTTGCTGATAAAGTTTATTTTTTACCATTAACACCT
GAATATGTTGAGCAAGTCATTAAAGCTGAAAGACCATCAGGAATTTTATTAAGTTTTGGA
GGACAAACAGCATTAAATTGCGGTGTTGAACTTGAAAAGAAGGGAATTTTGAAGAAATAC
AATATAAATGTGCTTGGCACACAAATCAGCTCAATTGTCGAAACAGAAGATAGAAAACTT
TTTGCTGATCGTGTAAATGAGATTGGTGAAAAAGTTGCACCGTCAGCAGCTGTCTATTCT
GTCGCGGAAGCATTACAAGCTGCTGAAAAAATTGGTTATCCAGTTATGGCTAGAGCTGCT
TTTTCATTAGGCGGTCTTGGTTCAGGTTTTGCTAGTAATCAAGATGAATTAAAGACTTTA
GCTCAACAAGCTCTATCATATTCAAATCAATTGATTATCGACAAATCACTTAAAGGATGG
AAAGAAGTTGAATACGAGGTTGTACGTGATGCTTATGATAATTGCATTACTGTTTGTAAC
ATGGAAAATGTCGATCCACTTGGGATTCATACGGGAGAGTCGATTGTTGTTGCTCCGTCT
CAAACACTTTCTAATCGCGAGTACAATATGCTTCGAACTACTGCCCTTAAAGTAATTCGT
CATTTTAATATCGTTGGAGAGTGTAATATTCAATATGCACTCAATCCAAACTCTGAAGAA
TATTACATTATTGAAGTAAATGCTCGATTGAGTAGAAGCTCAGCTCTTGCTAGTAAGGCG
ACCGGCTATCCGCTCGCATATGTTGCTGCAAAATTATCTCTCGGAATTCCTTTGCCAGAG
ATTAGAAATTCAGTTACTGGAGTAACAACTGCATGCTTTGAACCGTCACTTGATTATTGT
GTAGTCAAAATTCCGCGCTGGGACTTATCGAAATTCATTCGTGTTAGTAAAAATATTGGC
AGCTCAATGAAAAGTGTTGGTGAAGTTATGGCAATTGGAAGAAAGTTTGAAGAAGCTTTT
CAAAAAGCATTACGTATGGTTGATGAAAGTGTCAATGGTTTCGATCCTAATTTGAAACCT
GTAAATGATGAAGAATTAAAGACACCAACTGATAAGAGAATGTTTGTATTAGCAGCAGCT
TTAAAAGCGGGTTATTCGATTGACAAACTTTATGATTTGACAAAAATTGATCGGTGGTTC
TTATCAAAAATGAAAAATATAATTGACATTACTCTCGAGTTAGAGAAACTAAATTGTGCA
ATCCCTGAAGATCTTCTAAAAGAAGCAAAGAATCATGGATTTTCAGATAAACAAATTGCG
AAATTCATCAAAGGATCTGAATTAGCAGTGAGAAAGCAAAGGCGTGAATGTAATATTATT
CCATTTGTCAAACAGATCGATACTGTCGCAGGAGAGTGGCCTGCGTCAACAAATTATTTG
TATTTAACTTACAACGCCTCAACACATGACGTTGAGTTCAACGAACAAATGATTATGGTG
ATTGGTTCTGGTGTTTATCGAATTGGATCAAGTGTAGAATTTGACTGGTGTGCTGTTGGA
TGCCTAAGAGAATTAAGAAATCTTGGAAAGAAGACAATAATGGTCAATTACAATCCTGAG
ACTGTTTCAACTGACTATGACATGAGTGATCGTTTATATTTTGAAGAAATTTCATTTGAG
ACAGTTATGGACATTTATTCGAATGAAGATGCAGAAGGAATAATTTTGAGTATGGGAGGA
CAATTGCCTAATAATATTGCAATGGACTTACATCGTCAACATGCAAGAATTCTTGGCACA
AGCCCTGAATCAGTTGATTCGGCTGAAAATCGTTTCAAATTTTCAAGATTGTTAGATCGC
AAAGGAATCTCACAGCCACGATGGAAAGAGCTTACAAATCTACAATCAGCAACAGAATTT
TGTGAAGAAGTCGGCTATCCATGCCTTGTTCGTCCGTCGTATGTTCTTTCCGGCGCAGCT
ATGAATGTCGCATACTCTCATCAAGATCTTGAGACATATTTACATGCAGCATCAATTGTC
AGCAAAGATCATCCCGTTGTTATTTCAAAATTCTTAACTGAAGCAAAAGAAATCGATGTC
GATGCAGTTGCTGATGATGGTGAAATTTTGTGTCTTGCTGTTTCAGAACATGTTGAGAAT
GCAGGAGTTCATTCCGGAGATGCGACCTTAGTAACACCACCACAAGACATCAACAAAGAA
ACACTTGAGAAAATTAAAGGAATTGCTAAAGATATTGCTGCATTGCTCGATATTTCCGGA
CCTTTCAACATGCAATTGATTGCCAAAAATAACGAGCTCAAAGTCATTGAATGCAATGTC
AGAGTTTCACGTTCTTTTCCTTTCGTCTCGAAAACCCTCAATCATGATTTTGTGGCAATG
GCAACTCGTGTCATTATTGGTGAAAAAGTTGATCCCGTCGATGTGTTGCATAGTGAAAAT
TCAAAAGTTGGTGTGAAAGTTCCACAATTCAGTTTTTCACGTCTCGCTGGTGCTGAAGTA
ACACTGGGTGTTGAAATGAGTTCAACTGGCGAGGTTGCGTGTTTTGGTGATAATCGATAT
GAAGCATATTTGAAAGCAATGATGTCAACTGGATTCCAAATGCCCAAAAAATCAATTCTT
ATCAGTGTTGGAAGTATTCGACATAAAAATGAACTTTTGACATCAATTCGTGACTTGGCA
CGCATGGGTTACAAATTAATTTAA

>g13252.t1 Gene=g13252 Length=1347
MTNDVCLVLEDGTILSGQKFGADRDVDGEVVFQTGMVGYIESMTDPSYHGQILVLTYPLI
GNYGVPTETEFDENQLIKHFESDNKIWISGLIVGELCDDPSHWRLKYKLAEWMKKHNVAG
ISGIDTRALTKQIRENGTVLGKIVQQPSGPFLGIEFKDQNERNLVAEVSTKVAKTYNANG
SPRICAVDCGLKLNQIRCFIKRGARVDVVPWDHPLNPKDFDGLFLSNGPGDPVMCHKTVK
NIQQVLASSNAKPIFGICLGHQLLSTAIGCKTYKMKYGNRGHNLPALHHGTNRCFMTSQN
HGFAVDATTIDNANWEPLFTNLNDNSNEGIVHKEKPYFSVQFHPEHTAGPEDLECLFDVF
LDSVKDNMKNVTGLSIKNRLLKKLIYVPKVQLERRPKKVLILGSGGLSIGQAGEFDYSGS
QAIKAMQEEKIQTVLINPNIATVQTSKGLADKVYFLPLTPEYVEQVIKAERPSGILLSFG
GQTALNCGVELEKKGILKKYNINVLGTQISSIVETEDRKLFADRVNEIGEKVAPSAAVYS
VAEALQAAEKIGYPVMARAAFSLGGLGSGFASNQDELKTLAQQALSYSNQLIIDKSLKGW
KEVEYEVVRDAYDNCITVCNMENVDPLGIHTGESIVVAPSQTLSNREYNMLRTTALKVIR
HFNIVGECNIQYALNPNSEEYYIIEVNARLSRSSALASKATGYPLAYVAAKLSLGIPLPE
IRNSVTGVTTACFEPSLDYCVVKIPRWDLSKFIRVSKNIGSSMKSVGEVMAIGRKFEEAF
QKALRMVDESVNGFDPNLKPVNDEELKTPTDKRMFVLAAALKAGYSIDKLYDLTKIDRWF
LSKMKNIIDITLELEKLNCAIPEDLLKEAKNHGFSDKQIAKFIKGSELAVRKQRRECNII
PFVKQIDTVAGEWPASTNYLYLTYNASTHDVEFNEQMIMVIGSGVYRIGSSVEFDWCAVG
CLRELRNLGKKTIMVNYNPETVSTDYDMSDRLYFEEISFETVMDIYSNEDAEGIILSMGG
QLPNNIAMDLHRQHARILGTSPESVDSAENRFKFSRLLDRKGISQPRWKELTNLQSATEF
CEEVGYPCLVRPSYVLSGAAMNVAYSHQDLETYLHAASIVSKDHPVVISKFLTEAKEIDV
DAVADDGEILCLAVSEHVENAGVHSGDATLVTPPQDINKETLEKIKGIAKDIAALLDISG
PFNMQLIAKNNELKVIECNVRVSRSFPFVSKTLNHDFVAMATRVIIGEKVDPVDVLHSEN
SKVGVKVPQFSFSRLAGAEVTLGVEMSSTGEVACFGDNRYEAYLKAMMSTGFQMPKKSIL
ISVGSIRHKNELLTSIRDLARMGYKLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
42 g13252.t1 CDD cd01744 GATase1_CPSase 184 361 1.67142E-94
40 g13252.t1 Gene3D G3DSA:3.50.30.20 Carbamoyl phosphate synthetase 3 152 3.1E-58
36 g13252.t1 Gene3D G3DSA:3.40.50.880 - 159 367 3.0E-57
38 g13252.t1 Gene3D G3DSA:3.40.50.20 - 391 505 1.9E-49
34 g13252.t1 Gene3D G3DSA:3.30.470.20 - 509 786 4.5E-124
41 g13252.t1 Gene3D G3DSA:1.10.1030.10 Carbamoyl Phosphate Synthetase; Chain A 787 899 5.2E-35
39 g13252.t1 Gene3D G3DSA:3.40.50.20 - 901 1039 9.9E-58
35 g13252.t1 Gene3D G3DSA:3.30.470.20 - 1043 1306 1.2E-100
37 g13252.t1 Gene3D G3DSA:3.30.1490.20 - 1063 1132 1.2E-100
8 g13252.t1 Hamap MF_01209 Carbamoyl-phosphate synthase small chain [carA]. 3 368 40.283409
6 g13252.t1 PANTHER PTHR11405 CARBAMOYLTRANSFERASE FAMILY MEMBER 60 1347 0.0
7 g13252.t1 PANTHER PTHR11405:SF5 CAD PROTEIN 60 1347 0.0
9 g13252.t1 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 184 198 6.4E-35
13 g13252.t1 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 220 234 6.4E-35
22 g13252.t1 PRINTS PR00096 Glutamine amidotransferase superfamily signature 223 232 5.2E-11
25 g13252.t1 PRINTS PR00097 Anthranilate synthase component II signature 223 232 3.7E-6
11 g13252.t1 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 253 269 6.4E-35
23 g13252.t1 PRINTS PR00096 Glutamine amidotransferase superfamily signature 253 264 5.2E-11
26 g13252.t1 PRINTS PR00097 Anthranilate synthase component II signature 253 264 3.7E-6
10 g13252.t1 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 270 287 6.4E-35
12 g13252.t1 PRINTS PR00099 Carbamoyl-phosphate synthase protein GATase domain signature 295 306 6.4E-35
21 g13252.t1 PRINTS PR00096 Glutamine amidotransferase superfamily signature 339 352 5.2E-11
24 g13252.t1 PRINTS PR00097 Anthranilate synthase component II signature 339 352 3.7E-6
20 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 408 422 2.2E-65
17 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 437 447 2.2E-65
15 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 557 569 2.2E-65
19 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 591 610 2.2E-65
16 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 626 643 2.2E-65
14 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 683 712 2.2E-65
18 g13252.t1 PRINTS PR00098 Carbamoyl-phosphate synthase protein CPSase domain signature 765 783 2.2E-65
1 g13252.t1 Pfam PF00988 Carbamoyl-phosphate synthase small chain, CPSase domain 6 143 2.6E-51
2 g13252.t1 Pfam PF00117 Glutamine amidotransferase class-I 187 361 3.9E-44
4 g13252.t1 Pfam PF02786 Carbamoyl-phosphate synthase L chain, ATP binding domain 517 720 6.2E-81
3 g13252.t1 Pfam PF02787 Carbamoyl-phosphate synthetase large chain, oligomerisation domain 804 881 1.2E-28
5 g13252.t1 Pfam PF02786 Carbamoyl-phosphate synthase L chain, ATP binding domain 1071 1251 6.5E-25
47 g13252.t1 ProSitePatterns PS00867 Carbamoyl-phosphate synthase subdomain signature 2. 683 690 -
45 g13252.t1 ProSitePatterns PS00866 Carbamoyl-phosphate synthase subdomain signature 1. 1086 1100 -
46 g13252.t1 ProSitePatterns PS00867 Carbamoyl-phosphate synthase subdomain signature 2. 1215 1222 -
50 g13252.t1 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile. 183 370 26.913
52 g13252.t1 ProSiteProfiles PS50975 ATP-grasp fold profile. 522 714 40.133
51 g13252.t1 ProSiteProfiles PS50975 ATP-grasp fold profile. 1055 1246 41.863
44 g13252.t1 SMART SM01097 CPSase_sm_chain_2 3 144 4.6E-79
43 g13252.t1 SMART SM01096 CPSase_L_D3_2 802 924 6.2E-60
29 g13252.t1 SUPERFAMILY SSF52021 Carbamoyl phosphate synthetase, small subunit N-terminal domain 5 151 5.75E-52
33 g13252.t1 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like 156 367 3.7E-56
28 g13252.t1 SUPERFAMILY SSF52440 PreATP-grasp domain 393 516 2.59E-42
32 g13252.t1 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 517 786 1.29E-97
30 g13252.t1 SUPERFAMILY SSF48108 Carbamoyl phosphate synthetase, large subunit connection domain 781 931 2.48E-51
27 g13252.t1 SUPERFAMILY SSF52440 PreATP-grasp domain 933 1051 5.9E-43
31 g13252.t1 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 1050 1309 7.95E-87
49 g13252.t1 TIGRFAM TIGR01368 CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit 6 365 1.3E-132
48 g13252.t1 TIGRFAM TIGR01369 CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit 394 1347 0.0

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:0006541 glutamine metabolic process BP
GO:0046872 metal ion binding MF
GO:0006807 nitrogen compound metabolic process BP
GO:0005524 ATP binding MF
GO:0006207 ‘de novo’ pyrimidine nucleobase biosynthetic process BP
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) 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