General information for g12958.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 g12958 is located on chr_1: 27160108..27162079 (- 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_1 | g12958 | g12958.t1 | TTS | g12958.t1 | 27160069 | 27160069 |
| chr_1 | g12958 | g12958.t1 | isoform | g12958.t1 | 27160108 | 27162079 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon1 | 27160108 | 27160310 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS1 | 27160108 | 27160310 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon2 | 27160375 | 27160579 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS2 | 27160375 | 27160579 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon3 | 27160634 | 27161064 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS3 | 27160634 | 27161064 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon4 | 27161144 | 27161507 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS4 | 27161144 | 27161507 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon5 | 27161695 | 27161966 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS5 | 27161695 | 27161966 |
| chr_1 | g12958 | g12958.t1 | exon | g12958.t1.exon6 | 27162022 | 27162079 |
| chr_1 | g12958 | g12958.t1 | cds | g12958.t1.CDS6 | 27162022 | 27162079 |
| chr_1 | g12958 | g12958.t1 | TSS | g12958.t1 | 27162124 | 27162124 |
Sequences
>g12958.t1 Gene=g12958 Length=1533
ATGGCTAAATTTTCATTATTTTTCACGTTTATTGTGATAATTTCTTCAGTTTTTGGAGAC
GAATATCACAATCATAAGACAAAGTCTTTAAGAAAAACTTCTAAAGCATTTAATGAAGCT
GAAAAGACAACAGAATATTGGGTATCACAAGGGCAAGATAAATTAAAGGAACTCGTAAAC
AGAAAATACAACAACAATAATGCTAAAAATGTGATTTTCTTTCTGGGTGATGGTATGAGC
ATCACTACAATTTCAGCCGCTCGTACGTTACTTGGAGGAGAAGAAAAGAATTTATATTTT
GATAATTTTCCCTATACTGGATATTCTAAGACTTACTGCGTTGATGCTCAAGTAGCTGAT
TCAGCATGTACAGCGACTGCTTATCTAACGGGAGTAAAAAATAATTATGAAACAATTGGT
ATTACTGCGAAAGCCAAAGTCCAAGATTGTGATGCTCATGTGAACAAAGAATTATGGACT
GAAAGTATCGTGCGTTGGGCTCAAAAGACATGCAAAGCAACTGGAATTGTGACCACTACA
CGAATTACTCATGCCAGTCCTGCTGGAGCCTACGCACACACAGTTGAACGTGATTGGGAA
AATGACTTTGAAGTTTCAAACAATAAATGTGATGCTGATAAGGTTGATGATATTGCTGAA
CAATTAATTTATAATATTGAAGGAAAAAATCTAAATGGAAAAGATTTAATTGAAGAATGG
AAATCAGCTCGTGGAAGTAAAGCTTCTTATATTTGGAATAATATACAATTAAAGGCTATT
GATTATGAAAATACTGACTACATTCTTGGTCTTTTTGAGCATGACCATATGAAATACAAT
AAAGATGTTGTAGCAAATAATTTGGGAAATAGTGAACCAACATTAAGTGAAATGACTGAA
GCAGCAATAAAAATGCTACAAAAAGAAGAAAATGGGTACTTTTTGTTCATTGAAGGTGGA
ATGATTGATCAAGCTCATCATTATAATTATGCACAATTAGCTTTAGATGAAACTGATCAA
TTTCAAAAGGCAATTGAAGTTGCACACAAAATGACTAATAATGATGAAACTTTGATAGTT
GTTACAGCTGATCATTCACATGTTTTTACTTACAATGGCTATCCTCCACGTGGAAGTCCA
ATCTTTGAAGCAGTTGAAATAAGTGATGTTGACGATCTTCCATACACAACTTTAAGTTAT
GCCAATGGACCTGGTTATGAATTCATGTTTGACACAAATGGAAATCGCAAAAATCCAGCA
ACTTTTGATTTTAAAAATTATAAACTTCAATATCCAGCAACTGTTCCACTTTCCAAAGAA
ACTCATGGAGGTGAAGATGTTGCTGTCTATGCAACTGGTCCAATGGCTCATCTATTTAAT
GGACATTATGAACAAAATACTATACCTTTAATTATGGCTTACATTCTTAAAGTTGGACCA
TACGCTGTTGATGAAAAATGTACATCTTGTGCCACAATGCCAATCTTAATTTTAACTTTA
GTTATGATTTTAATTGTTAAATTATTAAAATAA
>g12958.t1 Gene=g12958 Length=510
MAKFSLFFTFIVIISSVFGDEYHNHKTKSLRKTSKAFNEAEKTTEYWVSQGQDKLKELVN
RKYNNNNAKNVIFFLGDGMSITTISAARTLLGGEEKNLYFDNFPYTGYSKTYCVDAQVAD
SACTATAYLTGVKNNYETIGITAKAKVQDCDAHVNKELWTESIVRWAQKTCKATGIVTTT
RITHASPAGAYAHTVERDWENDFEVSNNKCDADKVDDIAEQLIYNIEGKNLNGKDLIEEW
KSARGSKASYIWNNIQLKAIDYENTDYILGLFEHDHMKYNKDVVANNLGNSEPTLSEMTE
AAIKMLQKEENGYFLFIEGGMIDQAHHYNYAQLALDETDQFQKAIEVAHKMTNNDETLIV
VTADHSHVFTYNGYPPRGSPIFEAVEISDVDDLPYTTLSYANGPGYEFMFDTNGNRKNPA
TFDFKNYKLQYPATVPLSKETHGGEDVAVYATGPMAHLFNGHYEQNTIPLIMAYILKVGP
YAVDEKCTSCATMPILILTLVMILIVKLLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g12958.t1 | CDD | cd16012 | ALP | 69 | 477 | 1.98246E-111 |
| 13 | g12958.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 41 | 228 | 3.7E-71 |
| 12 | g12958.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 229 | 488 | 2.2E-96 |
| 3 | g12958.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 26 | 232 | 2.6E-174 |
| 5 | g12958.t1 | PANTHER | PTHR11596:SF85 | AT01495P-RELATED | 26 | 232 | 2.6E-174 |
| 2 | g12958.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 227 | 484 | 2.6E-174 |
| 4 | g12958.t1 | PANTHER | PTHR11596:SF85 | AT01495P-RELATED | 227 | 484 | 2.6E-174 |
| 7 | g12958.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 68 | 88 | 9.1E-42 |
| 9 | g12958.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 118 | 133 | 9.1E-42 |
| 6 | g12958.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 167 | 187 | 9.1E-42 |
| 8 | g12958.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 294 | 323 | 9.1E-42 |
| 1 | g12958.t1 | Pfam | PF00245 | Alkaline phosphatase | 68 | 477 | 4.6E-117 |
| 16 | g12958.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 17 | g12958.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 18 | g12958.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 20 | g12958.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 15 | g12958.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 490 | - |
| 19 | g12958.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 491 | 509 | - |
| 14 | g12958.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 510 | 510 | - |
| 22 | g12958.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 118 | 126 | - |
| 23 | g12958.t1 | SMART | SM00098 | alk_phosph_2 | 69 | 479 | 1.8E-154 |
| 10 | g12958.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 41 | 482 | 8.18E-138 |
| 11 | g12958.t1 | SignalP_EUK | 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. There were no conditions that were differentially expressed