General information for g11859.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GPI mannosyltransferase 3.
Parent gene
- The parent gene g11859 is located on chr_1: 18796715..18797861 (- 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 | g11859 | g11859.t1 | TTS | g11859.t1 | 18795749 | 18795749 |
| chr_1 | g11859 | g11859.t1 | isoform | g11859.t1 | 18796120 | 18797861 |
| chr_1 | g11859 | g11859.t1 | exon | g11859.t1.exon1 | 18796120 | 18797216 |
| chr_1 | g11859 | g11859.t1 | cds | g11859.t1.CDS1 | 18796120 | 18797216 |
| chr_1 | g11859 | g11859.t1 | exon | g11859.t1.exon2 | 18797269 | 18797594 |
| chr_1 | g11859 | g11859.t1 | cds | g11859.t1.CDS2 | 18797269 | 18797594 |
| chr_1 | g11859 | g11859.t1 | exon | g11859.t1.exon3 | 18797734 | 18797861 |
| chr_1 | g11859 | g11859.t1 | cds | g11859.t1.CDS3 | 18797734 | 18797861 |
| chr_1 | g11859 | g11859.t1 | TSS | g11859.t1 | 18797889 | 18797889 |
Sequences
>g11859.t1 Gene=g11859 Length=1551
ATGTCAACAATTTTTGTGATTTTTCTATTATTATTTGTAAGAATCGCGTCAGTTTTTCTC
GTACAAACTTTCTTTAGTCCTGATGAATATTGGCAAAGTGTGGAAGTTAGTCATCGTATG
GTCTTCAATTATGGACATCTTACATGGGAATGGATTCAAGGAATTCGAAGTTATTTTTAC
CCGACGCTCTTTGCAGCCATTTACAAAGTTCTTGATATTTTAAAAATAGACTCACGCGTC
TTTTTGATTCTCCTACCGAGAATATTTCAAGCTCTCATCTCAACCTACGCAGATTATCGT
TTCTATAACTGGTGTAACCGCAAAAAATGGTCACTTTTTATCATCATTACTAGCTGGTTT
TGGTTTTATACTGCAAGCAGAACTTTGATAAATTCATTTGAAGCTTCTCTTACAACAATC
GCTTTAAGTTTCTTTCCTTGGAACAAATTTGATGAAAATACTGGATTTTTGTGGATCACT
GCTTTATTGTCATTTATTCGACCAACATCGATTGTCACATGGTTACCTTTATGTATTTAT
CACGTAAAAAAATCAAAATATCCAGTTTGGGAATTGTTGATTAAACGCTATTTGTTTATT
GGACTTGTAACTGGAGGAGCATTAATTGCACTAGATTCTTTCTTCCATGGATCATTCATA
GTTACACCATATGAGTTCATTAAAATCAACGTTTTTGAAGGAATAGCTAGTTTTTATGGT
ACTCATCCATTTTACTGGTATTTTAGCACAGGACTGCCTGCTATTCTTGGTATTGGAATA
GTTCCATTCTATTTATCAATTTTTACAACAATCAAACGATCATGGGATCAATCGACAATT
GCAATTATGACTTCAATTATATTGACCATTTTCATGTACTCTCTACTGCCACACAAAGAA
TTTAGATTTTTGCTTCAAATACTGCCACTTTGTCTTTACTGTATTACACAATTCCTGTCA
GAATGGAGTAGAACAAAGTCATCACTCGTCATTTGGTTTGTAGCTATAGTCATTTTTATA
AGCAATGCAGTGCCAGCTGGATATCTCGGTTTCGTTCATCAACAAGGAACAATAAAAGTT
ATGGATCAAGTTTCTTCAATTGCAAACAACTATAAAACACAAGACGGACATCCAGCAAAA
ATATTTTTCATGATGCCATGTCATTCAACGCCTTTTTATTCACACGTCCATAAAAACATT
ACAATGAGATTCCTCACTTGTGAGCCTAATCTTAACAATCAGTTGAATTATGTAGATGAA
GCTGATAAATTTTATGAAGCTCCAATGAAATGGATTCGAAGTCATTTACCGGTACATCCA
GTGAATGCATTGCCAACTCACGTTGTGGTATTCGACACTCTAGTACCAATGATCAGTGAT
TTTCTTTCACTCTATAAACCAATCGAAATTTTCTTCCATGCTGATCATCTCGTCTCACAA
CGTGCAGGACATAACGTTTTAATTTATGAGCGTAATGAACAAGAAGTCAAGAAAAAGGAA
GAGGAGAAAGTTATTAAGCAAAAAGATCAAAAAGTTCCGGATGAGCTTTAA
>g11859.t1 Gene=g11859 Length=516
MSTIFVIFLLLFVRIASVFLVQTFFSPDEYWQSVEVSHRMVFNYGHLTWEWIQGIRSYFY
PTLFAAIYKVLDILKIDSRVFLILLPRIFQALISTYADYRFYNWCNRKKWSLFIIITSWF
WFYTASRTLINSFEASLTTIALSFFPWNKFDENTGFLWITALLSFIRPTSIVTWLPLCIY
HVKKSKYPVWELLIKRYLFIGLVTGGALIALDSFFHGSFIVTPYEFIKINVFEGIASFYG
THPFYWYFSTGLPAILGIGIVPFYLSIFTTIKRSWDQSTIAIMTSIILTIFMYSLLPHKE
FRFLLQILPLCLYCITQFLSEWSRTKSSLVIWFVAIVIFISNAVPAGYLGFVHQQGTIKV
MDQVSSIANNYKTQDGHPAKIFFMMPCHSTPFYSHVHKNITMRFLTCEPNLNNQLNYVDE
ADKFYEAPMKWIRSHLPVHPVNALPTHVVVFDTLVPMISDFLSLYKPIEIFFHADHLVSQ
RAGHNVLIYERNEQEVKKKEEEKVIKQKDQKVPDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11859.t1 | Coils | Coil | Coil | 489 | 511 | - |
| 2 | g11859.t1 | PANTHER | PTHR22760 | GLYCOSYLTRANSFERASE | 8 | 490 | 3.0E-130 |
| 3 | g11859.t1 | PANTHER | PTHR22760:SF4 | GPI MANNOSYLTRANSFERASE 3 | 8 | 490 | 3.0E-130 |
| 1 | g11859.t1 | Pfam | PF03901 | Alg9-like mannosyltransferase family | 6 | 397 | 2.1E-103 |
| 22 | g11859.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 23 | g11859.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 24 | g11859.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 33 | g11859.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 20 | - |
| 17 | g11859.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 79 | - |
| 27 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 99 | - |
| 16 | g11859.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 100 | 110 | - |
| 29 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 111 | 130 | - |
| 19 | g11859.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 131 | 154 | - |
| 32 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 155 | 177 | - |
| 15 | g11859.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 178 | 196 | - |
| 26 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 197 | 224 | - |
| 21 | g11859.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 225 | 243 | - |
| 31 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 267 | - |
| 14 | g11859.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 268 | 278 | - |
| 30 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 279 | 297 | - |
| 18 | g11859.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 298 | 302 | - |
| 28 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 303 | 322 | - |
| 13 | g11859.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 323 | 328 | - |
| 25 | g11859.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 329 | 351 | - |
| 20 | g11859.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 352 | 516 | - |
| 11 | g11859.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 5 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 4 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 110 | 129 | - |
| 10 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 155 | 177 | - |
| 8 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 198 | 220 | - |
| 7 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 245 | 267 | - |
| 9 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 279 | 296 | - |
| 6 | g11859.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 330 | 352 | - |
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:0006506 | GPI anchor biosynthetic process | BP |
| GO:0000026 | alpha-1,2-mannosyltransferase activity | MF |
| GO:0004376 | glycolipid mannosyltransferase activity | MF |
| GO:0016757 | glycosyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05286 (GPI mannosyltransferase 3 [EC:2.4.1.-])
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.
