General information for g3083.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 g3083 is located on chr_3: 22607650..22608125 (+ 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 | g3083 | g3083.t1 | TSS | g3083.t1 | 22606112 | 22606112 |
| chr_3 | g3083 | g3083.t1 | isoform | g3083.t1 | 22606166 | 22608125 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon1 | 22606166 | 22606665 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS1 | 22606166 | 22606665 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon2 | 22606722 | 22606792 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS2 | 22606722 | 22606792 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon3 | 22606863 | 22607321 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS3 | 22606863 | 22607321 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon4 | 22607378 | 22607788 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS4 | 22607378 | 22607788 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon5 | 22607851 | 22607932 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS5 | 22607851 | 22607932 |
| chr_3 | g3083 | g3083.t1 | exon | g3083.t1.exon6 | 22607987 | 22608125 |
| chr_3 | g3083 | g3083.t1 | cds | g3083.t1.CDS6 | 22607987 | 22608125 |
| chr_3 | g3083 | g3083.t1 | TTS | g3083.t1 | 22608245 | 22608245 |
Sequences
>g3083.t1 Gene=g3083 Length=1662
ATGAAAATAATTTTATTATTTGCTTTTTTCCAAATAAATATTTTGTTAAACCATGCGGCT
GTTTATCAAACACCAAATCCAGACGATAAGCAATATTGGCATGAATATAATATAAATTAT
TTAAAAAACATTTTAAAGTCACAAAAGCCAACAAAAGTAGCAAAAAATGTAATTTTATTT
GTCGGTGATGGAATGTCATTTGCAACGATTGCTGCGGGCAGAATTCTTAAAGGACAAATG
CAAGGAAAATCAGGAGAAGAAACTCAAGTGAACTTTGAAACATTTCCACATATTGGCTTA
TCAAAGACTTATAATACCAATAGTCAAGTTCCAGATTCAGCTGCGACGGCAACCGCAATA
TTCTCAGGAATTAAAACAACGATAAGAACAATTGGTCTCAATAATCCAACACCAAATGCA
AAAGAAAGTGAACGTTTAAAAACAATAATTGATTGGGCACAAGAGAAAGGAAAAAGAACG
GGACTTGTGACGAATACAAGAATTTGTCATGCTACGCCTGCTTCTGCTTATGCATACAGT
TTTCATAGAGATTACGAATGTGACACAAAAGTACCAAATTATATTAGGTCACATTTCAAG
GACATATCAAGACAACTTGTAGAAAATAAACCCGGGAAAGATTTGAATGTGATTTTCGGA
GGCGGAAAAGATTTTTTGGGTGCACATGATATTTTTGAAAAGAATATTGTCCAATTCGCA
GGAGCTGGAGAAGTCTCGTGCAATCGTACTGATAAGCAAAATTTAGTAGAAAAATATTTA
CGACAATTTAATAATGAAACAGTAGTGAAATATGTGACAAATACGGGTGAAATGTTGGGC
ATTGACTATGATAATGTCGATCACGTGTTAGGATTATTTGCTAATAATCATATGGAATAT
GAAAGCCTGAGAAATAAAAATTCTGATGGACAGCCGTCACTGACAGAAATGACAAAAGCT
GCAATAAGAATTTTAAATAATAAAAAGAATAAAAATGGTTATGTTTTAATCGTTGAAGGC
GGTAAAATTGATCAAGCACATCATCAAAATCATGCTCGTCTTGCACTTGAAGAATTTGTT
GAATTTGAAAGAGCAATACAGCAAGCAAAAGATATGACATCCTCGGATGAAACTCTAATT
ATTGTAACAGCAGACCATGCACATAGCATGATATTTAATGGCTATGGAAAAAGAGGCAAT
GATATTCTAGGATTTGGAAATACGAAGAAAGTAAATAGTCAGCTATATGAGACGATTGTT
TATGCTACTGGTCCTGGCTATCTTTATCACACAAAGAACGACACTGATCCGACAATCAGT
CATATGATACCACTTGAAGAGTATACAGAAGAGCAAAGAGGTGATGCTCTATACATGCAT
CAGTCTATGATACCAATGTATGACTCTGTTCATGGTGGTGAAGATGTTGGAGTGTTTTCA
GATGGACCAGGATCATTTTTACTACAGAGAACTTTTGAACAATGTTATATTGCTTATGCG
ATATCTTTTGCAAGTTGTATTGGTCCTGCTGCTGACATGAATGAATTATGCAAGTCTAAA
CCAGAAAGGTTGACAAGTGATTCATCAAGTTTAAAAACATCAATAGGCCTAACGTTTTTA
TCAGTTTTATTCTGTAGTTTTAAATTCATTGCATCATTTTGA
>g3083.t1 Gene=g3083 Length=553
MKIILLFAFFQINILLNHAAVYQTPNPDDKQYWHEYNINYLKNILKSQKPTKVAKNVILF
VGDGMSFATIAAGRILKGQMQGKSGEETQVNFETFPHIGLSKTYNTNSQVPDSAATATAI
FSGIKTTIRTIGLNNPTPNAKESERLKTIIDWAQEKGKRTGLVTNTRICHATPASAYAYS
FHRDYECDTKVPNYIRSHFKDISRQLVENKPGKDLNVIFGGGKDFLGAHDIFEKNIVQFA
GAGEVSCNRTDKQNLVEKYLRQFNNETVVKYVTNTGEMLGIDYDNVDHVLGLFANNHMEY
ESLRNKNSDGQPSLTEMTKAAIRILNNKKNKNGYVLIVEGGKIDQAHHQNHARLALEEFV
EFERAIQQAKDMTSSDETLIIVTADHAHSMIFNGYGKRGNDILGFGNTKKVNSQLYETIV
YATGPGYLYHTKNDTDPTISHMIPLEEYTEEQRGDALYMHQSMIPMYDSVHGGEDVGVFS
DGPGSFLLQRTFEQCYIAYAISFASCIGPAADMNELCKSKPERLTSDSSSLKTSIGLTFL
SVLFCSFKFIASF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g3083.t1 | CDD | cd16012 | ALP | 55 | 506 | 5.36268E-107 |
| 11 | g3083.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 27 | 515 | 2.5E-160 |
| 2 | g3083.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 17 | 532 | 1.2E-190 |
| 3 | g3083.t1 | PANTHER | PTHR11596:SF83 | ALKALINE PHOSPHATASE 4 | 17 | 532 | 1.2E-190 |
| 7 | g3083.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 54 | 74 | 6.6E-36 |
| 8 | g3083.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 110 | 125 | 6.6E-36 |
| 6 | g3083.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 153 | 173 | 6.6E-36 |
| 4 | g3083.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 214 | 224 | 6.6E-36 |
| 5 | g3083.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 315 | 344 | 6.6E-36 |
| 1 | g3083.t1 | Pfam | PF00245 | Alkaline phosphatase | 54 | 507 | 7.8E-114 |
| 15 | g3083.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 16 | g3083.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 17 | g3083.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 20 | g3083.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 14 | g3083.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 495 | - |
| 18 | g3083.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 496 | 513 | - |
| 12 | g3083.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 514 | 533 | - |
| 19 | g3083.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 534 | 551 | - |
| 13 | g3083.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 552 | 553 | - |
| 23 | g3083.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 110 | 118 | - |
| 24 | g3083.t1 | SMART | SM00098 | alk_phosph_2 | 55 | 508 | 1.1E-143 |
| 9 | g3083.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 30 | 512 | 7.2E-130 |
| 10 | g3083.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 22 | g3083.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
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.
