General information for g1978.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Adenylosuccinate synthetase.
Parent gene
- The parent gene g1978 is located on chr_3: 14175617..14176064 (+ strand)
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_3 | g1978 | g1978.t1 | TSS | g1978.t1 | 14170301 | 14170301 |
| chr_3 | g1978 | g1978.t1 | isoform | g1978.t1 | 14170363 | 14175675 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon1 | 14170363 | 14170572 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS1 | 14170363 | 14170572 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon2 | 14171681 | 14171783 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS2 | 14171681 | 14171783 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon3 | 14172083 | 14172368 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS3 | 14172083 | 14172368 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon4 | 14172471 | 14172610 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS4 | 14172471 | 14172610 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon5 | 14172678 | 14172731 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS5 | 14172678 | 14172731 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon6 | 14172807 | 14172973 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS6 | 14172807 | 14172973 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon7 | 14173051 | 14173235 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS7 | 14173051 | 14173235 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon8 | 14173296 | 14173527 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS8 | 14173296 | 14173527 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon9 | 14174042 | 14174051 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS9 | 14174042 | 14174051 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon10 | 14174272 | 14174283 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS10 | 14174272 | 14174283 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon11 | 14174772 | 14174834 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS11 | 14174772 | 14174834 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon12 | 14175073 | 14175494 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS12 | 14175073 | 14175494 |
| chr_3 | g1978 | g1978.t1 | exon | g1978.t1.exon13 | 14175559 | 14175675 |
| chr_3 | g1978 | g1978.t1 | cds | g1978.t1.CDS13 | 14175559 | 14175675 |
| chr_3 | g1978 | g1978.t1 | TTS | g1978.t1 | 14176066 | 14176066 |
Sequences
>g1978.t1 Gene=g1978 Length=2001
ATGGCATCATCAACGCTAAATGGAGAAATCAATAATATAAACTACACAGATGATGTTATT
TCCCGTAATCGTTCTGGATCTTTAACTGGATCAGTTAGTAGTTATTCAAACAAGGTTTTA
GTAGTACTCGGTGCACAATGGGGAGATGAAGGGAAGGGAAAAGTCGTGGATATGCTTTCA
GTCAACGCTGACGTTGTTTGTAGATGTCAAGGCGGTAATAATGCAGGACATACAGTTGTC
GTTGATGGAAAGGAATTTGATTTTCATCTTTTGCCGAGTGGAATAATCAATGAAAAAAGC
ATATCTATAATTGGCAATGGAGTTGTTGTACATCTTCCTGGCTTATTTGAGGAATTGGCA
AAGAATGAGGCAAAAGGCTTATCAGATTGGCAAAATCGTTTGATTGTCTCTGACAGAGCT
CATTTGGTTTTTGATTTTCATCAACAAGTTGATGGATTGCAAGAGGCAGAAAAATGTAGA
GAAGGAAAATCACTTGGCACAACGAAAAAGGGCATTGGTCCAGCCTATTCTTCGAAAGCC
ACACGTAATGGCATTCGAGTTGGAGACTTGCTTGGTGATTTCAACACATTTAGTGACAAA
TTTCGTTCAATTGTTGCTACTCATCAACGTTTGTTTCCTGGCTGTGTCGTTGATGTTGAA
GCAGAACTCACTCGATATCAACAGTATGCTGAAAAATTACGACCTTATGTGAAAGACACC
ATCTTTTATCTTCATTCTGCATTGCGAAATGGCAAGACTGTTTTGGTCGAAGGAGCAAAT
GCGGCAATGTTGGATATCGATTTTGGAACATATCCTTATGTGACGAGTAGTAATTGCTCA
ATCGGTGGCGTTTTAACAGGTCTCGGTTTGCCGCCAAAAGTTATTGGAGAAGTCATTGGT
GTTGTTAAGTCATATACGACAAGAGTCGGTGATGGACCATTCCCCACAGAATTAAAAGAT
GACATTGGTGAACTTTTACAAACGCGTGGTGGAGAAATTGGTGTCACAACAAAACGAAAA
CGTCGTTGTGGTTGGTTGGATTTACCTGTGTTACGATATACCTCACTTGTCAATGGTTAT
TCAGCAATTTGCTTAACGAAACTTGATATCCTTGATACTTTGCCTACAATTAAAATTGGC
ATCAATTATAAATTACATAACAAAACGATCTACAATTTTCCTGGATCTATTTCTGATTTG
GCTCAAGTTGAGGTCGAATATGTTACACTCCCTGGTTGGCAACAATCGACTGCAAATATT
CGCGACTTTCGTGACCTACCCGAAAATGCACAAAACTATGTGCGATTTATTGAGAAGGAT
TTGGATGTTCCAATTAAGTGGATTGGAGTTGGAAAAGGGCGAGAATCAATTATTAAATAT
AAAAGTGTTGGTTTAAGAGATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTC
ACTGGTGTTTTAGGATATTTGGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGA
TTAGATAATGCTGGTAAAACAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAA
CATGTTCCAACACTTCATCCAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACA
ACTTTCGATTTAGGTGGTCACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCT
GTTGATGCAATTGTCTTCTTAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAA
AATGAATTGGATTCATTGTTAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTG
GGAAATAAAATTGACAAACCGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGA
CTTTATCAACTTACAACAGGAAAGGGAAAAATTTCAAGATCAGATTTAGCAGGCCGTCCA
TTAGAACTTTTTATGTGCTCGGTGCTGAAGAGACAAGGATATGGTGAAGGTTTTCGCTGG
TTAGCTCAATATATCGATTAA
>g1978.t1 Gene=g1978 Length=666
MASSTLNGEINNINYTDDVISRNRSGSLTGSVSSYSNKVLVVLGAQWGDEGKGKVVDMLS
VNADVVCRCQGGNNAGHTVVVDGKEFDFHLLPSGIINEKSISIIGNGVVVHLPGLFEELA
KNEAKGLSDWQNRLIVSDRAHLVFDFHQQVDGLQEAEKCREGKSLGTTKKGIGPAYSSKA
TRNGIRVGDLLGDFNTFSDKFRSIVATHQRLFPGCVVDVEAELTRYQQYAEKLRPYVKDT
IFYLHSALRNGKTVLVEGANAAMLDIDFGTYPYVTSSNCSIGGVLTGLGLPPKVIGEVIG
VVKSYTTRVGDGPFPTELKDDIGELLQTRGGEIGVTTKRKRRCGWLDLPVLRYTSLVNGY
SAICLTKLDILDTLPTIKIGINYKLHNKTIYNFPGSISDLAQVEVEYVTLPGWQQSTANI
RDFRDLPENAQNYVRFIEKDLDVPIKWIGVGKGRESIIKYKSVGLRDYSKLFTMFIWDWF
TGVLGYLGLWKKSGKLLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELSIGNMRFT
TFDLGGHTQARRVWKDYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALSNCPVLIL
GNKIDKPGAASEDELRNFYGLYQLTTGKGKISRSDLAGRPLELFMCSVLKRQGYGEGFRW
LAQYID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g1978.t1 | CDD | cd03108 | AdSS | 38 | 458 | 0.0 |
| 21 | g1978.t1 | CDD | cd00879 | Sar1 | 475 | 665 | 5.76803E-131 |
| 15 | g1978.t1 | Gene3D | G3DSA:3.40.440.10 | Adenylosuccinate Synthetase | 41 | 295 | 8.1E-111 |
| 16 | g1978.t1 | Gene3D | G3DSA:1.10.300.10 | Adenylosuccinate Synthetase | 138 | 236 | 8.1E-111 |
| 14 | g1978.t1 | Gene3D | G3DSA:3.90.170.10 | Adenylosuccinate Synthetase | 302 | 460 | 9.0E-66 |
| 13 | g1978.t1 | Gene3D | G3DSA:3.40.50.300 | - | 494 | 665 | 1.1E-58 |
| 5 | g1978.t1 | Hamap | MF_00011 | Adenylosuccinate synthetase [purA]. | 1 | 485 | 173.866226 |
| 3 | g1978.t1 | PANTHER | PTHR11846 | ADENYLOSUCCINATE SYNTHETASE | 28 | 460 | 1.0E-198 |
| 4 | g1978.t1 | PANTHER | PTHR11846:SF2 | ADENYLOSUCCINATE SYNTHETASE ISOZYME 1 | 28 | 460 | 1.0E-198 |
| 10 | g1978.t1 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 495 | 518 | 4.7E-67 |
| 9 | g1978.t1 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 523 | 547 | 4.7E-67 |
| 6 | g1978.t1 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 550 | 575 | 4.7E-67 |
| 7 | g1978.t1 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 595 | 616 | 4.7E-67 |
| 8 | g1978.t1 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 639 | 663 | 4.7E-67 |
| 1 | g1978.t1 | Pfam | PF00709 | Adenylosuccinate synthetase | 41 | 458 | 5.0E-177 |
| 2 | g1978.t1 | Pfam | PF00025 | ADP-ribosylation factor family | 481 | 665 | 1.6E-62 |
| 18 | g1978.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 470 | - |
| 19 | g1978.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 471 | 489 | - |
| 17 | g1978.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 490 | 666 | - |
| 25 | g1978.t1 | ProSitePatterns | PS01266 | Adenylosuccinate synthetase GTP-binding site. | 46 | 53 | - |
| 26 | g1978.t1 | ProSitePatterns | PS00513 | Adenylosuccinate synthetase active site. | 171 | 182 | - |
| 29 | g1978.t1 | ProSiteProfiles | PS51422 | small GTPase SAR1 family profile. | 487 | 665 | 31.336 |
| 23 | g1978.t1 | SMART | SM00788 | adenylsucc_synt | 39 | 459 | 2.9E-258 |
| 22 | g1978.t1 | SMART | SM00177 | arf_sub_2 | 476 | 653 | 1.5E-17 |
| 24 | g1978.t1 | SMART | SM00178 | sar_sub_1 | 477 | 665 | 3.5E-112 |
| 12 | g1978.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 37 | 459 | 2.16E-160 |
| 11 | g1978.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 490 | 665 | 9.5E-45 |
| 28 | g1978.t1 | TIGRFAM | TIGR00184 | purA: adenylosuccinate synthase | 41 | 461 | 1.3E-156 |
| 27 | g1978.t1 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 492 | 614 | 6.3E-15 |
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:0006886 | intracellular protein transport | BP |
| GO:0006164 | purine nucleotide biosynthetic process | BP |
| GO:0005525 | GTP binding | MF |
| GO:0004019 | adenylosuccinate synthase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01939 (adenylosuccinate synthase)
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.
