General information for g16715.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alkaline phosphatase 4.
Parent gene
- The parent gene g16715 is located on chr_4: 10627789..10630213 (- 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 | g16715 | g16715.t1 | isoform | g16715.t1 | 10627789 | 10630213 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon1 | 10627789 | 10627912 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS1 | 10627789 | 10627912 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon2 | 10627973 | 10628054 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS2 | 10627973 | 10628054 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon3 | 10628355 | 10628753 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS3 | 10628355 | 10628753 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon4 | 10628812 | 10629270 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS4 | 10628812 | 10629270 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon5 | 10629330 | 10629400 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS5 | 10629330 | 10629400 |
| chr_4 | g16715 | g16715.t1 | exon | g16715.t1.exon6 | 10629714 | 10630213 |
| chr_4 | g16715 | g16715.t1 | cds | g16715.t1.CDS6 | 10629714 | 10630213 |
| chr_4 | g16715 | g16715.t1 | TSS | g16715.t1 | NA | NA |
| chr_4 | g16715 | g16715.t1 | TTS | g16715.t1 | NA | NA |
Sequences
>g16715.t1 Gene=g16715 Length=1635
ATGAAATTACTCTTTTTACTTGCATTTTTTCAATTTAATATTTTGCTAAGTCATTCAGCC
ATTTATCAATCACCAAATAAAGAAGATAAACAATTTTGGCATGAATACAATGTGAATTAT
TTGAAAAATATTTTAAAATCACAAAAGCCAACAAAAGTAGCAAAAAATGTCATTTTATTT
GTTGGCGATGGAATGTCATTTGCAACAATTACAGCTGGTAGAATTCTCAAAGGACAAATG
CAAGGAAAATCAGGAGAAGAAACTAAAATAAATTTTGAATCATTTCCGTATCTTGGATTA
GCAAAAACTTACACTACAACCACTCAAGTCCCAGATTCAGCTGCAACAGCCACTGCAATA
TTTTCAGGAATCAAAACATCAACAAGAACAATTGGTCTAAGTAATCCAACAATAAATGCA
AAAGAACATGAACGTTTGCCAACAATAATTGATTGGGCACAAGAAAAAGGGAAAAGAACG
GGACTGGTGACAACTACAAGAATCACTCATGCTACACCTGCTGCTGCTTATGCATACAGT
TTTGATAGATTATACGAGTGTGATACAAAAGTTCCAAATGAGATTAAATCACATTTCAAA
GACATGTCAAGACAGCTCGTAGAAAATAAACCTGGCAAAGACATGAACGTGATTTTTGGA
GGAGGGAAAGATTTTTTAGGAGCTCATGATATTTTTGAAAAAAACGTTGTGCAATTTGCA
GGTCCATCAGAAATTTCATGTGATCGTACAGATAAAGTAAATTTAATTGAAAAATATTTA
CAACAATTTAGTAACGAAACATCAGTGAAATATGTGAAAAATACTGGTGAATTGTTGGCT
ATTGATTATGATAATGTTGATCATGTGTTAGGAATTTTTGCCAATAATCATTTAGAATAT
GAAAGTTTAAAAAATAAAAATCCTGATGGACAACCATCATTAACACAAATGACTGAAGCG
GCAATTAAAATTTTGAATAATAAAAAGAATCAAAATGGCTTTGTTTTAATTGTTGAAAGT
GGTAAAATTGACCATGCACATCATCAAAATCATGCTCGCCTTGCATTAGAAGAATTTGTA
GAATTAGAGAAATCAATTCAACAAGCAATCAACATGACATCATCGGATGAAACTTTAATT
ATCGTCACATCAGACCATGGACATAATATGATTTTTAATGGTCGTCCAAAAAGAGGTGAT
GACATTCTGGGCTTTGCAAATACAAAAAATGGAAATAATCAACTTTATGAGACTCTAACT
TATGGCACTGGTCCTGGTTTTAATTATCATACAAAGAACAATACTGAAACTATAAAACCA
CTTGAAGAATATTCAGAAAAACAACGAAGCCATCCTTTATATATGCATCAGTCTATGGTA
CCATTGATAGAATCAACTCATGGCGGTGAAGATGTTGGAGTATTTTCAGATGGACCAGGA
TCATTTTTATTGCAAAGAACTTTCGAGCAGTGCTATATTGGCTATGCTATATCTTTTGCA
AGTTGTATTGGTCCTGTTGCTGACATGAATGAATTGTGTAAATCTAAACAGGAAAAATTA
ACAAGTGATTCATTAAGTTTGAAAATGTCAATAAGTCCAATGTTGTTATCAGCTTATTTC
ATAGTTTTAAATTAA
>g16715.t1 Gene=g16715 Length=544
MKLLFLLAFFQFNILLSHSAIYQSPNKEDKQFWHEYNVNYLKNILKSQKPTKVAKNVILF
VGDGMSFATITAGRILKGQMQGKSGEETKINFESFPYLGLAKTYTTTTQVPDSAATATAI
FSGIKTSTRTIGLSNPTINAKEHERLPTIIDWAQEKGKRTGLVTTTRITHATPAAAYAYS
FDRLYECDTKVPNEIKSHFKDMSRQLVENKPGKDMNVIFGGGKDFLGAHDIFEKNVVQFA
GPSEISCDRTDKVNLIEKYLQQFSNETSVKYVKNTGELLAIDYDNVDHVLGIFANNHLEY
ESLKNKNPDGQPSLTQMTEAAIKILNNKKNQNGFVLIVESGKIDHAHHQNHARLALEEFV
ELEKSIQQAINMTSSDETLIIVTSDHGHNMIFNGRPKRGDDILGFANTKNGNNQLYETLT
YGTGPGFNYHTKNNTETIKPLEEYSEKQRSHPLYMHQSMVPLIESTHGGEDVGVFSDGPG
SFLLQRTFEQCYIGYAISFASCIGPVADMNELCKSKQEKLTSDSLSLKMSISPMLLSAYF
IVLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g16715.t1 | CDD | cd16012 | ALP | 55 | 502 | 4.23448E-103 |
| 12 | g16715.t1 | Coils | Coil | Coil | 543 | 544 | - |
| 11 | g16715.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 27 | 512 | 5.8E-158 |
| 2 | g16715.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 18 | 525 | 5.8E-185 |
| 3 | g16715.t1 | PANTHER | PTHR11596:SF83 | ALKALINE PHOSPHATASE 4 | 18 | 525 | 5.8E-185 |
| 7 | g16715.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 54 | 74 | 1.4E-37 |
| 8 | g16715.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 110 | 125 | 1.4E-37 |
| 6 | g16715.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 153 | 173 | 1.4E-37 |
| 4 | g16715.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 214 | 224 | 1.4E-37 |
| 5 | g16715.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 315 | 344 | 1.4E-37 |
| 1 | g16715.t1 | Pfam | PF00245 | Alkaline phosphatase | 54 | 503 | 1.1E-112 |
| 16 | g16715.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 17 | g16715.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 18 | g16715.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 10 | - |
| 21 | g16715.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 11 | 19 | - |
| 14 | g16715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 491 | - |
| 19 | g16715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 492 | 513 | - |
| 13 | g16715.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 514 | 524 | - |
| 20 | g16715.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 525 | 542 | - |
| 15 | g16715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 543 | 544 | - |
| 25 | g16715.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 110 | 118 | - |
| 24 | g16715.t1 | SMART | SM00098 | alk_phosph_2 | 55 | 504 | 3.3E-148 |
| 9 | g16715.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 29 | 508 | 1.43E-126 |
| 10 | g16715.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 23 | g16715.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
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. There were no conditions that were differentially expressed