General information for g17204.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative N-acetylneuraminate lyase.
Parent gene
- The parent gene g17204 is located on chr_4: 12812932..12813783 (+ 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_4 | g17204 | g17204.t1 | TSS | g17204.t1 | 12812884 | 12812884 |
| chr_4 | g17204 | g17204.t1 | isoform | g17204.t1 | 12812932 | 12813783 |
| chr_4 | g17204 | g17204.t1 | exon | g17204.t1.exon1 | 12812932 | 12813783 |
| chr_4 | g17204 | g17204.t1 | cds | g17204.t1.CDS1 | 12812932 | 12813783 |
| chr_4 | g17204 | g17204.t1 | TTS | g17204.t1 | 12813824 | 12813824 |
Sequences
>g17204.t1 Gene=g17204 Length=852
ATGTCATCATTAAAATTGGTCAAGTTTGAAGGTTTAATGGCTCCAACATTTACGCCTTTT
GATGAGAATAATCAAGTAAATTACGACATTATTGAACCATATGCAAAATTTTTAAAATCA
AATGGAATTGAAGCAATTTTAATCAATGGCACAACAGGTGAAGGAATGTTAATGACAGTT
GAAGAACGTAAGAAAGTCACTGAAAAATGGCAAGAAGTTTGTAAAAAGTTAGAAATTCTC
ATGATGGTCCAGATTGCTGGCTGCTCTTTTGCTGATGTTATTGAACTTGCAAAACATGCT
GAAAAAATTGAAGTCGATGGAGTTTTGTGTCTACCTGAACTTTATTTTAAACCTAAAACA
ATTGAAAAACTTGTTGGATATTTAAAGGAAATTTCAAAATTTTGTCCAACTCGTCCACTT
TATTATTATCATATTCCGATGTTTGTAAGTGTTGATGTTCCAATGGCTGCTTTTATGGAA
CTTGCAAAGAAAGAAATTTCAACATTTAAAGGCATCAAATTTACATCTGGTGATTTAGAA
AAAGGATTTCCATGTTTAAAACATGGACAAGTTTATTTGGGAAGCGATACGATCTTATGT
GGTGCACTTGCATTGGGTTTCACTTCTGCAATTATGACATCACTCAATATTGTGCCTCAT
TTGGCTATAAAAATTGTTGAATACATGAAAAAAGGAGAAGTTGAAAAGGCAAGAGAACAA
CAAATGCTTTTGACTGAATTTGTTGAAAAAATTTTAAAAAAAGGAGGAGGCGACTGGGTG
CCATCAATGAAAAAAGCTTTTAATGAAAATTTTAAAGATATGAATTTAGGATGTGTTAGA
AAACCTTTGTAA
>g17204.t1 Gene=g17204 Length=283
MSSLKLVKFEGLMAPTFTPFDENNQVNYDIIEPYAKFLKSNGIEAILINGTTGEGMLMTV
EERKKVTEKWQEVCKKLEILMMVQIAGCSFADVIELAKHAEKIEVDGVLCLPELYFKPKT
IEKLVGYLKEISKFCPTRPLYYYHIPMFVSVDVPMAAFMELAKKEISTFKGIKFTSGDLE
KGFPCLKHGQVYLGSDTILCGALALGFTSAIMTSLNIVPHLAIKIVEYMKKGEVEKAREQ
QMLLTEFVEKILKKGGGDWVPSMKKAFNENFKDMNLGCVRKPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g17204.t1 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 6 | 283 | 2.8E-72 |
| 2 | g17204.t1 | PANTHER | PTHR12128:SF21 | N-ACETYLNEURAMINATE LYASE | 5 | 283 | 4.0E-84 |
| 3 | g17204.t1 | PANTHER | PTHR12128 | DIHYDRODIPICOLINATE SYNTHASE | 5 | 283 | 4.0E-84 |
| 8 | g17204.t1 | PIRSF | PIRSF001365 | DHDPS | 4 | 270 | 3.4E-49 |
| 4 | g17204.t1 | PRINTS | PR00146 | Dihydrodipicolinate synthase signature | 42 | 63 | 3.4E-7 |
| 5 | g17204.t1 | PRINTS | PR00146 | Dihydrodipicolinate synthase signature | 138 | 155 | 3.4E-7 |
| 1 | g17204.t1 | Pfam | PF00701 | Dihydrodipicolinate synthetase family | 8 | 254 | 2.9E-35 |
| 9 | g17204.t1 | ProSitePatterns | PS00665 | Dihydrodipicolinate synthase signature 1. | 45 | 62 | - |
| 10 | g17204.t1 | SMART | SM01130 | DHDPS_2 | 8 | 283 | 1.1E-40 |
| 6 | g17204.t1 | SUPERFAMILY | SSF51569 | Aldolase | 8 | 283 | 4.08E-61 |
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:0016829 | lyase activity | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01639 (N-acetylneuraminate 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.
