General information for g417.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alkaline phosphatase, tissue-nonspecific isozyme.
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.t1 | TSS | g417.t1 | 3294794 | 3294794 |
| chr_3 | g417 | g417.t1 | isoform | g417.t1 | 3295001 | 3297563 |
| chr_3 | g417 | g417.t1 | exon | g417.t1.exon1 | 3295001 | 3295503 |
| chr_3 | g417 | g417.t1 | cds | g417.t1.CDS1 | 3295001 | 3295503 |
| chr_3 | g417 | g417.t1 | exon | g417.t1.exon2 | 3296151 | 3296188 |
| chr_3 | g417 | g417.t1 | cds | g417.t1.CDS2 | 3296151 | 3296188 |
| chr_3 | g417 | g417.t1 | exon | g417.t1.exon3 | 3296247 | 3296780 |
| chr_3 | g417 | g417.t1 | cds | g417.t1.CDS3 | 3296247 | 3296780 |
| chr_3 | g417 | g417.t1 | exon | g417.t1.exon4 | 3296836 | 3297563 |
| chr_3 | g417 | g417.t1 | cds | g417.t1.CDS4 | 3296836 | 3297563 |
| chr_3 | g417 | g417.t1 | TTS | g417.t1 | NA | NA |
Sequences
>g417.t1 Gene=g417 Length=1803
ATGAGACTTGCTGTGATATACCGTGAGTTATTTTTACTGTTACTTACTTTAGCGACATGC
CGCAATGCTCCAACAACAAAAACAAATATTCACGATAAATCTTATTGGTATGACAAAAAT
TACAAATTAATTAATGATCGAATGGGATATTTGCAAGTCAATCATCTACCAAGAGTTAAG
AATGTTGTAATTTTTATTGGTGACGGAATGGGAACTTCAACAATAACCGCAAGTCGTGTT
TATAAGCGTCAAATATCACAAAATCCAAATGCTCGGTTGACATTTGATGATTTTCCTGCT
ACAGCAATTGTGCAAACTGACATCGAAAATTCACAAATTCCAGAATCAGCCGCAAGTAGC
ACTGCACTTTTCTGCGGTGTTAAAACAAACTATGAATATTTAGGAATTGATGTTACATCA
ACAGGCAAAAAAGTGTGTGAAGAAAAAAATTCACACACACCATCAATAATTTCTTGGGCA
CAAGAAAAAAACCTCAAAACAGGATTTGTGACGACAACTAGAGTAACTCATGCAACACCA
GCTTCATTATATGCTCATTCACGACGTCATATGGAAGATGATTCAAAGGGTGACACACAT
GGTTGCAAAGACGTAGCAAGACAGCTGATTGAAAATAAAACGGGCAAAAATTTAAATGTC
ATAATGGGTGGTGGAATGATGACTCTAATAAAAAGAGAAGAAGATGGCAGTGGCGGAAGA
AGAAAAGATGGAAAAAATTTGACAGCTGAATGGCTTTTGCATCATCCAAATGGCGAATTT
GTTACAAATCGTGATGAAATGATGAATATTAGTCATAAAACTGAACATGTTCTTGGAATT
TTTGCTAGAAGTCATATGGAATTTAATGCTGATCGTAATAAAAAAATTGAGCCATCATTA
GCGGAAATGACTTTGACTGCAATTGAAATTTTAAAAAGGAAAAATCAAAGAGGATTTTTA
TTAGTTGTTGAAGGTGGAAAAATTGATTTAGCTCATCATCAGAACCAAGCATATAGAGCA
TTAGATGATACATTGGCATTTGATGAAGCTATTAAAGTTGCTATGAAAAATTTAGATTTA
TCACAAACATTAATAATTGTCACATCTGATCATTCTTCAGCAATGTCTTATTCTGGCTTT
GCAACACCTAAAAATCAATCAATACTTGGAATGGACATATACATTTCAAATATTGATCAA
AAACCTTATCAAATTCTAACGTACAGTAGTGGAATTGGTTATCAAAATTACACTGAAGAA
ATAGCAATGAAAGATTTTAAAAATGCAATTCACAAATCGACTGTTCCTACAACCTGGTCA
AATCATGGTGGCGAAGATGTTCCTTTATATGCAATTGGTCCAATGTCAACACTTTTATTT
AGTGGAACTTTTGATCAGACTTATATGCCTCATGCAATCGCTTATGCAATGTGCATTTTT
AAATATGAATCAAGATGTCAACGTCAAAGTAATGAAATTCATAATGAAATTGAAAGACCA
CAAGTTGAAGAAAAAACATCAGGCATTGAAGCTCTTAGAAAAGAACTTTATAAAGCAAAA
AATGAAAATCAAACTGTGAAAATTGAAGAACAAACAGAAATTGAAAATATAACAATTTCA
ACAACGGAATCGAATTATGATGAAAATTTAAATAATGACACATTTTCAGATTCTCTTGTG
TTTGAATCATCAGATTTAGTAAGCAATTTAACTACAAATGATAATGAAAATTCATCATCT
AATGTTTTTTGCAATAGTTTTGTAGTTGTCATTTTAGTAACATTGTTATCAATAAAATTT
TAA
>g417.t1 Gene=g417 Length=600
MRLAVIYRELFLLLLTLATCRNAPTTKTNIHDKSYWYDKNYKLINDRMGYLQVNHLPRVK
NVVIFIGDGMGTSTITASRVYKRQISQNPNARLTFDDFPATAIVQTDIENSQIPESAASS
TALFCGVKTNYEYLGIDVTSTGKKVCEEKNSHTPSIISWAQEKNLKTGFVTTTRVTHATP
ASLYAHSRRHMEDDSKGDTHGCKDVARQLIENKTGKNLNVIMGGGMMTLIKREEDGSGGR
RKDGKNLTAEWLLHHPNGEFVTNRDEMMNISHKTEHVLGIFARSHMEFNADRNKKIEPSL
AEMTLTAIEILKRKNQRGFLLVVEGGKIDLAHHQNQAYRALDDTLAFDEAIKVAMKNLDL
SQTLIIVTSDHSSAMSYSGFATPKNQSILGMDIYISNIDQKPYQILTYSSGIGYQNYTEE
IAMKDFKNAIHKSTVPTTWSNHGGEDVPLYAIGPMSTLLFSGTFDQTYMPHAIAYAMCIF
KYESRCQRQSNEIHNEIERPQVEEKTSGIEALRKELYKAKNENQTVKIEEQTEIENITIS
TTESNYDENLNNDTFSDSLVFESSDLVSNLTTNDNENSSSNVFCNSFVVVILVTLLSIKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g417.t1 | CDD | cd16012 | ALP | 60 | 478 | 3.09069E-110 |
| 12 | g417.t1 | Coils | Coil | Coil | 502 | 529 | - |
| 11 | g417.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 31 | 487 | 3.4E-148 |
| 2 | g417.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 13 | 486 | 2.3E-143 |
| 3 | g417.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 59 | 79 | 3.7E-36 |
| 7 | g417.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 113 | 128 | 3.7E-36 |
| 4 | g417.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 160 | 180 | 3.7E-36 |
| 6 | g417.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 217 | 227 | 3.7E-36 |
| 5 | g417.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 300 | 329 | 3.7E-36 |
| 1 | g417.t1 | Pfam | PF00245 | Alkaline phosphatase | 60 | 479 | 1.9E-113 |
| 15 | g417.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 16 | g417.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 17 | g417.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 17 | - |
| 19 | g417.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 22 | - |
| 14 | g417.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 579 | - |
| 18 | g417.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 580 | 598 | - |
| 13 | g417.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 599 | 600 | - |
| 22 | g417.t1 | SMART | SM00098 | alk_phosph_2 | 60 | 480 | 7.2E-129 |
| 8 | g417.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 35 | 479 | 2.76E-121 |
| 10 | g417.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 21 | g417.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 9 | g417.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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 transcript has been annotated with K01077 (alkaline phosphatase)
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.
