General information for g3882.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Adenylosuccinate lyase.
Parent gene
- The parent gene g3882 is located on chr_3: 28608730..28610392 (- 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 | g3882 | g3882.t1 | isoform | g3882.t1 | 28608730 | 28610392 |
| chr_3 | g3882 | g3882.t1 | exon | g3882.t1.exon1 | 28608730 | 28608804 |
| chr_3 | g3882 | g3882.t1 | cds | g3882.t1.CDS1 | 28608730 | 28608804 |
| chr_3 | g3882 | g3882.t1 | exon | g3882.t1.exon2 | 28608978 | 28610195 |
| chr_3 | g3882 | g3882.t1 | cds | g3882.t1.CDS2 | 28608978 | 28610195 |
| chr_3 | g3882 | g3882.t1 | exon | g3882.t1.exon3 | 28610261 | 28610392 |
| chr_3 | g3882 | g3882.t1 | cds | g3882.t1.CDS3 | 28610261 | 28610392 |
| chr_3 | g3882 | g3882.t1 | TSS | g3882.t1 | NA | NA |
| chr_3 | g3882 | g3882.t1 | TTS | g3882.t1 | NA | NA |
Sequences
>g3882.t1 Gene=g3882 Length=1425
ATGGCAGAAAAGTATTATCGGTCGTGTTTATCAACTCGTTATGCTTCACACGAAATGCAG
TATTTATTTTCTGATCATTTCAAATATACAACATGGAGAAAACTCTGGATTTATCTGGCA
AAAGCACAAAAGGAACTTGGACTAAAAATTACTGATGAACAGATCAAAGAAATGGAGGAT
AATGTTGAAAACTTAAATTATGAAGAGATCGCAAAACAAGAAAAAATAACACGTCATGAA
GTGATTGCAAATATAAATGCTTTTTCTTCAGTTTGTAGCAAAGCTAAATCTATAATACAC
TCAGGAGCGACAAGCAATTACGTTGTTGATAATGCTGATTTAATTATAATACGTGAATCA
CTCGATATTATCTTAGTTCGGCTTGTGGCAATCATCAAATTTCTATCAGATTTTGCGCTT
GATTATAGTGCTCTACCTACATTAGGTTTTACTCATTTGCAAGCAGCTCAATTAACTACT
GTAGGCAAAAGATGCACTTTATGGATTCACGATTTACTTATGGATGAAAGAAATTTATCT
TTTATAAGAGAAAATTTGAAATTTCGTGGAGTAAAAGGAACAATTGGAACTCAAGCAAGT
TATTTAGAAAAATTTAATGGTGATCATGAAAAAGTTAAGCAACTCGAACGCTTAGTTACA
GCAATGGCGGGATTTGAAAAGAGTTATTCAATAACTGGTCAAACCTATTCGCGTAAAGTT
GATCTCGATATTATTGCAGCACTCTCTAGTCTAGGTTCGAGTGTTCATAAAATATGCACT
GACATTCGACTACTTGCTTCAAAAAAAGAAATCGAAGAGCCGTTTGAAAAGAGTCAAGTA
GGATCTTCAGCAATGCCTTATAAAAGAAATCCAATCAGATCAGAACGTTGTTGTGCCTTA
GCTCGACATTTAATTACACTTCATTCAAATGCTGCAAACACACATGCAACACAATGGATG
GAACGTACATTAGATGATTCAGCCAACCGTAGAATAACAATTGCTGAAAGCTTTTTAACT
GCAGATGCATGCTTGCTAATTCTATTAAATATATCGCAACAAGGTCTTGTCGTTTATCCA
AAAATCATTGAAAATCATATTAAACAAGAACTTCCTTTCATGGCAACTGAAAGTATTTTA
ACATCTATGGAAAAAATAGGAGTAGATCGTCAAGATTGCCACGAAAAACTTCGAGTTCTC
TCACAAGAAGCTTCAGCTCAAGTAAAACAATTTGGTTCAGAGAATGATTTGATTGAGCGC
ATTAAAAGCGATACTTATTTTGAGCCGATTTTCAATCAGTTAAGTAGCATTATGAATCCT
AATAATTTCACCGGAAGAGCTTCACAGCAGTCAAAAGCACACAAGAATTTTTATGATTTT
GAAATATGCAATGCATACACTCATGATGATCATCAGCAGCAATGA
>g3882.t1 Gene=g3882 Length=474
MAEKYYRSCLSTRYASHEMQYLFSDHFKYTTWRKLWIYLAKAQKELGLKITDEQIKEMED
NVENLNYEEIAKQEKITRHEVIANINAFSSVCSKAKSIIHSGATSNYVVDNADLIIIRES
LDIILVRLVAIIKFLSDFALDYSALPTLGFTHLQAAQLTTVGKRCTLWIHDLLMDERNLS
FIRENLKFRGVKGTIGTQASYLEKFNGDHEKVKQLERLVTAMAGFEKSYSITGQTYSRKV
DLDIIAALSSLGSSVHKICTDIRLLASKKEIEEPFEKSQVGSSAMPYKRNPIRSERCCAL
ARHLITLHSNAANTHATQWMERTLDDSANRRITIAESFLTADACLLILLNISQQGLVVYP
KIIENHIKQELPFMATESILTSMEKIGVDRQDCHEKLRVLSQEASAQVKQFGSENDLIER
IKSDTYFEPIFNQLSSIMNPNNFTGRASQQSKAHKNFYDFEICNAYTHDDHQQQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3882.t1 | CDD | cd03302 | Adenylsuccinate_lyase_2 | 10 | 446 | 0.0 |
| 12 | g3882.t1 | Coils | Coil | Coil | 48 | 75 | - |
| 10 | g3882.t1 | Gene3D | G3DSA:1.20.200.10 | Fumarase/aspartase (Central domain) | 13 | 450 | 3.4E-153 |
| 11 | g3882.t1 | Gene3D | G3DSA:1.10.275.60 | - | 24 | 235 | 3.4E-153 |
| 9 | g3882.t1 | Gene3D | G3DSA:1.10.40.30 | - | 369 | 443 | 3.4E-153 |
| 3 | g3882.t1 | PANTHER | PTHR43172 | ADENYLOSUCCINATE LYASE | 4 | 453 | 2.8E-183 |
| 6 | g3882.t1 | PRINTS | PR00149 | Fumarate lyase superfamily signature | 99 | 117 | 5.3E-15 |
| 4 | g3882.t1 | PRINTS | PR00149 | Fumarate lyase superfamily signature | 144 | 162 | 5.3E-15 |
| 7 | g3882.t1 | PRINTS | PR00149 | Fumarate lyase superfamily signature | 238 | 265 | 5.3E-15 |
| 5 | g3882.t1 | PRINTS | PR00149 | Fumarate lyase superfamily signature | 281 | 297 | 5.3E-15 |
| 1 | g3882.t1 | Pfam | PF00206 | Lyase | 39 | 298 | 2.6E-28 |
| 2 | g3882.t1 | Pfam | PF10397 | Adenylosuccinate lyase C-terminus | 372 | 450 | 3.0E-10 |
| 14 | g3882.t1 | ProSitePatterns | PS00163 | Fumarate lyases signature. | 281 | 290 | - |
| 15 | g3882.t1 | SMART | SM00998 | ADSL_C_2 | 371 | 455 | 7.2E-10 |
| 8 | g3882.t1 | SUPERFAMILY | SSF48557 | L-aspartase-like | 12 | 451 | 7.54E-93 |
| 16 | g3882.t1 | TIGRFAM | TIGR00928 | purB: adenylosuccinate lyase | 10 | 450 | 1.5E-114 |
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:0004018 | N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity | MF |
| GO:0009152 | purine ribonucleotide biosynthetic process | BP |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01756 (adenylosuccinate lyase)
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.
