General information for g12957.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Membrane-bound alkaline phosphatase.
Parent gene
- The parent gene g12957 is located on chr_1: 27160052..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 | g12957 | g12957.t1 | TSS | g12957.t1 | 27157972 | 27157972 |
| chr_1 | g12957 | g12957.t1 | isoform | g12957.t1 | 27157996 | 27160052 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon1 | 27157996 | 27158389 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS1 | 27157996 | 27158389 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon2 | 27158452 | 27158627 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS2 | 27158452 | 27158627 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon3 | 27158785 | 27158819 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS3 | 27158785 | 27158819 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon4 | 27158876 | 27159345 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS4 | 27158876 | 27159345 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon5 | 27159402 | 27159761 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS5 | 27159402 | 27159761 |
| chr_1 | g12957 | g12957.t1 | exon | g12957.t1.exon6 | 27159826 | 27160052 |
| chr_1 | g12957 | g12957.t1 | cds | g12957.t1.CDS6 | 27159826 | 27160052 |
| chr_1 | g12957 | g12957.t1 | TTS | g12957.t1 | 27160076 | 27160076 |
Sequences
>g12957.t1 Gene=g12957 Length=1662
ATGAAAACATTAAAATTCTTTACTTTTTCGGTATTTTTCATCGCAATTAGTAAAGGTGAA
GATGATTTTCATCCAAAGCCTTTAATTGAAATTGCACCTCATATTGAATTAAACGATGTC
GATTCACGTTTGAGAGATCTTGAGGGTTTTAATGAATATTGGAATAATAAGGCTCAAAAT
TACATCGCTGATCAATTAAAATCAAATTTGAATACCAAAAAAGCAAAAAATTTGATTTTA
TTTCTTGGTGATGGACTTTCAATTTCGACAGTAGCTGCAACTAGAATGTATTTAGGTGGA
GAAGAAGTTGAATTGGATTTCGAGAAATTTTCTCATTACGGCTTAGCAAAAACGTACTGC
GTTGACCGTCAAGTATCTGATTCAGCTTGTACTGCTACCGCGTTTTTATCTGGGGTAAAG
AATAATTATAGAAGTTTAGGGTTAACAGCGAATGTTTTAAGTAATCAATGTAACTTTAAC
GATTCTGATATTACTTATTCAATGCTAAAATGGGCACAAGATGCAGGAAAAGCCACAGGA
ATTGTAACCACAACTCGAATAACACATGCTACACCTGCAGGTGCTTATGCTCATAGTCCA
CACAGAGAATGGGAAAACAATGCAGCAATTTCGTCTACTTGTCGTAATTCAAATACAAGT
CGAATTGTCGATATTGCACATCAACTTATCTATAATGAAGAAGCTCAAAAATTCAAAGTC
ATTCTTGGTGGCGGTACAAGACATTTCCTCAATACTACAATGCAAAATGAAGAAGGTAGA
GCTGGTGAAAGAACTGATGGAAGAAATTTAATTGATGAATGGCTTCAAGAACGTAATAAA
ATAGGAAAAGCAAAATATTTTTGGCATAAGCAGCAACTTGATGAATTAAATGTTGATGAT
ACAGATTATTTGTTGGGATTATTTGAGCATGATCATCTTATGTATCGACTTGATGTTGTT
AATGCTAGATTACAAGCACAAGAGCCAATGTTGACTGATCTAACAAGGGCTGCTATCAAA
ATGCTTAAAAAGGAAGATAATGGCTTTGTACTCTTAGTTGAAGGAGGAAGAATTGATCAT
GCGCATCATTCAAATTATGCAAGAAAATCACTTGATGAAACTGCTGAATTTGCAAGAGCA
ATTGAACTGGCAAAACTGATGACAAATGAAGAGGAAACTTTGATAGTTGTTACATCAGAC
CATTCACATGTTTTTACATATGCTGGCTATCCATTACGCAAAAATGATGTTTTAAGAACT
GCAGGAAGAGGAGACGACAGAATGCCTTATGAAACTTTAAGTTATGCAAATGGTCCTGGC
TACGATAGAACATTTGATGAAAATGGAGTTAGAGCTAATATGACAGAAGATGATTTTTCC
TTTAGAAGTCGTCGTTATTCAGCTATGGTTTCACTTTCTTCTGAGACTCATGCTGGTGAA
GACGTTGGAGTCTATGCAAATGGACCTTGGTCACATCTCTTTCAAGGAAGTTATGAACAA
AATGTGATCCCAATTGCTATGGCGTATGCCGCAAAAATTGGCCCTTATGCTGATATTATT
TTAGAATCAACAACAACTCAATCAATGGCTAATGGAATTTATATCATGCCTGTTCTTTTG
ATCTTTGGTTTGATACTATCTGTATTTAAAATTTTGCTTTAA
>g12957.t1 Gene=g12957 Length=553
MKTLKFFTFSVFFIAISKGEDDFHPKPLIEIAPHIELNDVDSRLRDLEGFNEYWNNKAQN
YIADQLKSNLNTKKAKNLILFLGDGLSISTVAATRMYLGGEEVELDFEKFSHYGLAKTYC
VDRQVSDSACTATAFLSGVKNNYRSLGLTANVLSNQCNFNDSDITYSMLKWAQDAGKATG
IVTTTRITHATPAGAYAHSPHREWENNAAISSTCRNSNTSRIVDIAHQLIYNEEAQKFKV
ILGGGTRHFLNTTMQNEEGRAGERTDGRNLIDEWLQERNKIGKAKYFWHKQQLDELNVDD
TDYLLGLFEHDHLMYRLDVVNARLQAQEPMLTDLTRAAIKMLKKEDNGFVLLVEGGRIDH
AHHSNYARKSLDETAEFARAIELAKLMTNEEETLIVVTSDHSHVFTYAGYPLRKNDVLRT
AGRGDDRMPYETLSYANGPGYDRTFDENGVRANMTEDDFSFRSRRYSAMVSLSSETHAGE
DVGVYANGPWSHLFQGSYEQNVIPIAMAYAAKIGPYADIILESTTTQSMANGIYIMPVLL
IFGLILSVFKILL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g12957.t1 | CDD | cd16012 | ALP | 76 | 512 | 7.39259E-110 |
| 11 | g12957.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 48 | 520 | 2.1E-174 |
| 2 | g12957.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 48 | 525 | 2.8E-190 |
| 3 | g12957.t1 | PANTHER | PTHR11596:SF85 | AT01495P-RELATED | 48 | 525 | 2.8E-190 |
| 8 | g12957.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 75 | 95 | 2.9E-45 |
| 4 | g12957.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 125 | 140 | 2.9E-45 |
| 6 | g12957.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 172 | 192 | 2.9E-45 |
| 5 | g12957.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 237 | 247 | 2.9E-45 |
| 7 | g12957.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 330 | 359 | 2.9E-45 |
| 1 | g12957.t1 | Pfam | PF00245 | Alkaline phosphatase | 75 | 512 | 4.5E-122 |
| 14 | g12957.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 15 | g12957.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 16 | g12957.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 14 | - |
| 18 | g12957.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 13 | g12957.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 532 | - |
| 17 | g12957.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 533 | 552 | - |
| 12 | g12957.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 553 | 553 | - |
| 21 | g12957.t1 | ProSitePatterns | PS00123 | Alkaline phosphatase active site. | 125 | 133 | - |
| 22 | g12957.t1 | SMART | SM00098 | alk_phosph_2 | 76 | 514 | 2.2E-161 |
| 9 | g12957.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 51 | 518 | 6.38E-138 |
| 10 | g12957.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 20 | g12957.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 530 | 552 | - |
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