General information for g12960.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 g12960 is located on chr_1: 27164904..27170755 (- 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 | g12960 | g12960.t1 | TTS | g12960.t1 | 27163955 | 27163955 |
| chr_1 | g12960 | g12960.t1 | isoform | g12960.t1 | 27164904 | 27170755 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon1 | 27164904 | 27165157 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS1 | 27164904 | 27165157 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon2 | 27165213 | 27165297 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS2 | 27165213 | 27165297 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon3 | 27165349 | 27166295 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS3 | 27165349 | 27166295 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon4 | 27166348 | 27166599 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS4 | 27166348 | 27166599 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon5 | 27168850 | 27169056 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS5 | 27168850 | 27169056 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon6 | 27170145 | 27170666 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS6 | 27170145 | 27170666 |
| chr_1 | g12960 | g12960.t1 | exon | g12960.t1.exon7 | 27170719 | 27170755 |
| chr_1 | g12960 | g12960.t1 | cds | g12960.t1.CDS7 | 27170719 | 27170755 |
| chr_1 | g12960 | g12960.t1 | TSS | g12960.t1 | NA | NA |
Sequences
>g12960.t1 Gene=g12960 Length=2304
ATGTTTATGGGTGATGGCATGAGTCATTCAACTTTAGCCGCTACACGCATAGCATTGGGA
GGAGAAGACGTGAAACTCGCATTTGAAAATTTTCCACATACAGCGAGTTCAAAAACTTAT
TGTACAGATCAAGCAGTTGCTGATTCAGCTTGTACGATAACTGCTATGTTACATGGAATT
AAAACAAATGGAGGTATCGTTGGTTTAAATGGTGCAGCAGCGAACGACAGTTGTGAAGAT
CAAAATATAAAAAACAATCAAATTGAATCAATTGCTAAATGGTTTCAAGATCAAGACAGA
AGTGTCGGAGTTGTAACAAATACAAAGATAACTCATGCAACACCATCTGGTGTTTATGCG
AACATAGCAAATCGTAATTGGGAAGGAAATGCTGAAGTTATAAGAAGTGGCTGTGATCAT
TTAATGGTTGATGATATTGCTGAACAATTAGTTCATGGCAATATTGGTTCAAAATTAAAA
GTTGCTCTTGGTGGAGGTTCAAAATATTTCATAAACACATCAATGATTGAACATGGAAGT
AATGGTGCAAGAACTGATGATGACGTTCTAAGAATTTCGGATTTAGACATGCATCCTCAT
CTTGATACTACAAGATTTAAACCAAATAGTGCTGAATTGTCAAAAGACTTTTGGTTTAAT
AATGCTAAAAAATTCGTTGAAAATCAAGTTAAAAGAAATTTGAATACAAATACAGCAAAA
AATGTTATAATGTTTATGGGTGATGGCATGAGTCATTCAACTTTAGCTTCAACAGAACAA
TTTGAAGATGAATTTTCAAGAATTTCTGACTTGAATATGCAACCACATTTTGATGTTGAA
ACAACAGCAAATAAAATGACTTCCAGAGCCTTTACAAACAACATTGAATTGACAAAGGAT
TTTTGGATTGATAGTGCTAAAGATTTTGTTGCAAAACAAGTTAAAAAAAATTTAAATACA
AAGAAAGCAAAAAATATTATAATGTTTTTAGGTGATGGCATGGGCCATTCAACTTTAGCC
GCTACACGCATAGCATTAGGCGGAGAAGAAGTCAAACTGGCTTTTGAAAATTTTCCACAT
ACAGCGAGTTCAAAAACTTATTGTACAGATCAATCAGTTGCTGATTCAGCTTGTACGATA
ACTGCTATGTTACATGGAATTAAAACAAATGGAGGTATCGTTGGTTTAAATGCTGCAGCA
ACTCGTAACAGTTGTGAAGATCAAAATATAAAAAACAATCAAATTGAATCAATTGCTAAA
TGGTTTCAAGATCAAGACAGAAGTGTCGGAGTTGTGACAAATACAAAGATAACTCATGCA
ACACCATCTGGTGTTTATGCGAACATAGCAAATCGTAATTGGGAAGGAAATGCTGAAGTT
ATAAGAAGCGGTTGTGATCATTTAATGGTTGATGATATTGCTGAACAATTAGTTCATGGC
AATATTGGTTCAAAATTAAAAGTTGCACTTGGTGGAGGTTCAAAATATTTCATAAACACA
ACAATGATTGAAAATGGAAGTAATGGTGCAAGAACTGATGGCAAAAATTTAATTAATGAA
TGGCTTACAGCAAAAACAAATCGTCAATTTGTGAGAAACCGTGAAGAATTAATGAATGTT
GATATTAGAAAAATTGATCAATTATTGGGTTTATTCAGTACTCATCATATGCCTTATCAA
TTAGAAGTTAATGAGAACAATGAACAAAATATTTATCCAACTTTAACAGAAATGACTTTA
AAAGCAATTGAAATGCTTAGTAAAAATGATGATGGATATTTTCTATTAGTTGAAGGAGGT
AGAATCGACAATGCACAACATGCAACAAAAGCTAGACTTGTAATTGGAGAAATGATTGAA
TTCAATAATGCAATTGAAGCTGCTCTTAAAAAAATTGATTTGGAAGAGACTTTGGTTGTT
GTGACAGCTGACCATGGACATGCTTTGTCATTAGCTGGTTATTCTACAAGAAATGATGGT
GTTTTTGCAATGGGTGGGATTGCAAATGATGAACTACCTTTCTTAAAACTCTCGTTTTCT
AATGGAATGGGTTTCATAAAACATCACATTAATGGAATTCGAGTAAACGCTTCAGCTATT
GATACATCGTCAATTCATTTTCAATATCCGTCAACATTTCCGTTTAAATATGCAACGCAT
ACCGGAGAGGATGTTGGTGTTTGGGCAATTGGTCCATATTCGCATCTATTTAGTGGTACT
ATCGAACAAAACGTTATTGCTCATATTATGGCTTATGCTAGCTGTGTTGGAAAAGGGTTA
AAAGTTTGTAATAATAACGATTGA
>g12960.t1 Gene=g12960 Length=767
MFMGDGMSHSTLAATRIALGGEDVKLAFENFPHTASSKTYCTDQAVADSACTITAMLHGI
KTNGGIVGLNGAAANDSCEDQNIKNNQIESIAKWFQDQDRSVGVVTNTKITHATPSGVYA
NIANRNWEGNAEVIRSGCDHLMVDDIAEQLVHGNIGSKLKVALGGGSKYFINTSMIEHGS
NGARTDDDVLRISDLDMHPHLDTTRFKPNSAELSKDFWFNNAKKFVENQVKRNLNTNTAK
NVIMFMGDGMSHSTLASTEQFEDEFSRISDLNMQPHFDVETTANKMTSRAFTNNIELTKD
FWIDSAKDFVAKQVKKNLNTKKAKNIIMFLGDGMGHSTLAATRIALGGEEVKLAFENFPH
TASSKTYCTDQSVADSACTITAMLHGIKTNGGIVGLNAAATRNSCEDQNIKNNQIESIAK
WFQDQDRSVGVVTNTKITHATPSGVYANIANRNWEGNAEVIRSGCDHLMVDDIAEQLVHG
NIGSKLKVALGGGSKYFINTTMIENGSNGARTDGKNLINEWLTAKTNRQFVRNREELMNV
DIRKIDQLLGLFSTHHMPYQLEVNENNEQNIYPTLTEMTLKAIEMLSKNDDGYFLLVEGG
RIDNAQHATKARLVIGEMIEFNNAIEAALKKIDLEETLVVVTADHGHALSLAGYSTRNDG
VFAMGGIANDELPFLKLSFSNGMGFIKHHINGIRVNASAIDTSSIHFQYPSTFPFKYATH
TGEDVGVWAIGPYSHLFSGTIEQNVIAHIMAYASCVGKGLKVCNNND
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g12960.t1 | CDD | cd16012 | ALP | 324 | 755 | 0e+00 |
| 20 | g12960.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 1 | 213 | 0e+00 |
| 19 | g12960.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 214 | 294 | 0e+00 |
| 18 | g12960.t1 | Gene3D | G3DSA:3.40.720.10 | Alkaline Phosphatase | 296 | 764 | 0e+00 |
| 4 | g12960.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 1 | 206 | 0e+00 |
| 7 | g12960.t1 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 1 | 206 | 0e+00 |
| 3 | g12960.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 206 | 261 | 0e+00 |
| 6 | g12960.t1 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 206 | 261 | 0e+00 |
| 5 | g12960.t1 | PANTHER | PTHR11596 | ALKALINE PHOSPHATASE | 292 | 762 | 0e+00 |
| 8 | g12960.t1 | PANTHER | PTHR11596:SF75 | ALKALINE PHOSPHATASE-RELATED | 292 | 762 | 0e+00 |
| 13 | g12960.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 323 | 343 | 0e+00 |
| 11 | g12960.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 373 | 388 | 0e+00 |
| 12 | g12960.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 422 | 442 | 0e+00 |
| 9 | g12960.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 485 | 495 | 0e+00 |
| 10 | g12960.t1 | PRINTS | PR00113 | Alkaline phosphatase signature | 574 | 603 | 0e+00 |
| 2 | g12960.t1 | Pfam | PF00245 | Alkaline phosphatase | 1 | 187 | 0e+00 |
| 1 | g12960.t1 | Pfam | PF00245 | Alkaline phosphatase | 323 | 755 | 0e+00 |
| 17 | g12960.t1 | SMART | SM00098 | alk_phosph_2 | 324 | 757 | 0e+00 |
| 16 | g12960.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 1 | 187 | 0e+00 |
| 14 | g12960.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 211 | 265 | 1e-07 |
| 15 | g12960.t1 | SUPERFAMILY | SSF53649 | Alkaline phosphatase-like | 296 | 757 | 0e+00 |
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