General information for g417.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alkaline phosphatase.
Parent gene
- The parent gene g417 is located on chr_3: 3296247..3297563 (+ 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 | g417 | g417.t2 | isoform | g417.t2 | 3296247 | 3297563 |
| chr_3 | g417 | g417.t2 | exon | g417.t2.exon1 | 3296247 | 3296780 |
| chr_3 | g417 | g417.t2 | cds | g417.t2.CDS1 | 3296276 | 3296780 |
| chr_3 | g417 | g417.t2 | exon | g417.t2.exon2 | 3296836 | 3297563 |
| chr_3 | g417 | g417.t2 | cds | g417.t2.CDS2 | 3296836 | 3297563 |
| chr_3 | g417 | g417.t2 | TSS | g417.t2 | NA | NA |
| chr_3 | g417 | g417.t2 | TTS | g417.t2 | NA | NA |
Sequences
>g417.t2 Gene=g417 Length=1262
CTTCATTATATGCTCATTCACGACGTCATATGGAAGATGATTCAAAGGGTGACACACATG
GTTGCAAAGACGTAGCAAGACAGCTGATTGAAAATAAAACGGGCAAAAATTTAAATGTCA
TAATGGGTGGTGGAATGATGACTCTAATAAAAAGAGAAGAAGATGGCAGTGGCGGAAGAA
GAAAAGATGGAAAAAATTTGACAGCTGAATGGCTTTTGCATCATCCAAATGGCGAATTTG
TTACAAATCGTGATGAAATGATGAATATTAGTCATAAAACTGAACATGTTCTTGGAATTT
TTGCTAGAAGTCATATGGAATTTAATGCTGATCGTAATAAAAAAATTGAGCCATCATTAG
CGGAAATGACTTTGACTGCAATTGAAATTTTAAAAAGGAAAAATCAAAGAGGATTTTTAT
TAGTTGTTGAAGGTGGAAAAATTGATTTAGCTCATCATCAGAACCAAGCATATAGAGCAT
TAGATGATACATTGGCATTTGATGAAGCTATTAAAGTTGCTATGAAAAATTTAGATTTAT
CACAAACATTAATAATTGTCACATCTGATCATTCTTCAGCAATGTCTTATTCTGGCTTTG
CAACACCTAAAAATCAATCAATACTTGGAATGGACATATACATTTCAAATATTGATCAAA
AACCTTATCAAATTCTAACGTACAGTAGTGGAATTGGTTATCAAAATTACACTGAAGAAA
TAGCAATGAAAGATTTTAAAAATGCAATTCACAAATCGACTGTTCCTACAACCTGGTCAA
ATCATGGTGGCGAAGATGTTCCTTTATATGCAATTGGTCCAATGTCAACACTTTTATTTA
GTGGAACTTTTGATCAGACTTATATGCCTCATGCAATCGCTTATGCAATGTGCATTTTTA
AATATGAATCAAGATGTCAACGTCAAAGTAATGAAATTCATAATGAAATTGAAAGACCAC
AAGTTGAAGAAAAAACATCAGGCATTGAAGCTCTTAGAAAAGAACTTTATAAAGCAAAAA
ATGAAAATCAAACTGTGAAAATTGAAGAACAAACAGAAATTGAAAATATAACAATTTCAA
CAACGGAATCGAATTATGATGAAAATTTAAATAATGACACATTTTCAGATTCTCTTGTGT
TTGAATCATCAGATTTAGTAAGCAATTTAACTACAAATGATAATGAAAATTCATCATCTA
ATGTTTTTTGCAATAGTTTTGTAGTTGTCATTTTAGTAACATTGTTATCAATAAAATTTT
AA
>g417.t2 Gene=g417 Length=410
MEDDSKGDTHGCKDVARQLIENKTGKNLNVIMGGGMMTLIKREEDGSGGRRKDGKNLTAE
WLLHHPNGEFVTNRDEMMNISHKTEHVLGIFARSHMEFNADRNKKIEPSLAEMTLTAIEI
LKRKNQRGFLLVVEGGKIDLAHHQNQAYRALDDTLAFDEAIKVAMKNLDLSQTLIIVTSD
HSSAMSYSGFATPKNQSILGMDIYISNIDQKPYQILTYSSGIGYQNYTEEIAMKDFKNAI
HKSTVPTTWSNHGGEDVPLYAIGPMSTLLFSGTFDQTYMPHAIAYAMCIFKYESRCQRQS
NEIHNEIERPQVEEKTSGIEALRKELYKAKNENQTVKIEEQTEIENITISTTESNYDENL
NNDTFSDSLVFESSDLVSNLTTNDNENSSSNVFCNSFVVVILVTLLSIKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g417.t2 | CDD | cd16012 | ALP | 14 | 288 | 1.24044E-52 |
| 7 | g417.t2 | Coils | Coil | Coil | 312 | 339 | - |
| 6 | g417.t2 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 1 | 297 | 9.0E-93 |
| 2 | g417.t2 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 5 | 296 | 3.1E-87 |
| 3 | g417.t2 | PRINTS | PR00113 | Alkaline phosphatase signature | 27 | 37 | 1.0E-5 |
| 4 | g417.t2 | PRINTS | PR00113 | Alkaline phosphatase signature | 110 | 139 | 1.0E-5 |
| 1 | g417.t2 | Pfam | PF00245 | Alkaline phosphatase | 6 | 289 | 1.7E-69 |
| 9 | g417.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 389 | - |
| 10 | g417.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 390 | 408 | - |
| 8 | g417.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 409 | 410 | - |
| 12 | g417.t2 | SMART | SM00098 | alk_phosph_2 | 1 | 290 | 1.7E-24 |
| 5 | g417.t2 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 8 | 289 | 2.13E-72 |
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:0003824 | catalytic activity | MF |
| GO:0016791 | phosphatase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed