Gene loci information

Transcript annotation

  • This transcript has been annotated as GPI mannosyltransferase 3.

Parent gene

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.t7 TTS g11859.t7 18795749 18795749
chr_1 g11859 g11859.t7 isoform g11859.t7 18796120 18797861
chr_1 g11859 g11859.t7 exon g11859.t7.exon1 18796120 18797216
chr_1 g11859 g11859.t7 cds g11859.t7.CDS1 18796120 18797216
chr_1 g11859 g11859.t7 exon g11859.t7.exon2 18797269 18797594
chr_1 g11859 g11859.t7 cds g11859.t7.CDS2 18797269 18797594
chr_1 g11859 g11859.t7 exon g11859.t7.exon3 18797730 18797861
chr_1 g11859 g11859.t7 cds g11859.t7.CDS3 18797730 18797779
chr_1 g11859 g11859.t7 TSS g11859.t7 18797889 18797889

Sequences

>g11859.t7 Gene=g11859 Length=1555
ATGTCAACAATTTTTGTGATTTTTCTATTATTATTTGTAAGAATCGCGTCAGTTTTTCTC
GTACAAACTTTCTTTAGTCCTGATGAATATTGGCAAAGTGTGGAAGTTAGTCATCGTATG
GTCTTCAAGTAATTATGGACATCTTACATGGGAATGGATTCAAGGAATTCGAAGTTATTT
TTACCCGACGCTCTTTGCAGCCATTTACAAAGTTCTTGATATTTTAAAAATAGACTCACG
CGTCTTTTTGATTCTCCTACCGAGAATATTTCAAGCTCTCATCTCAACCTACGCAGATTA
TCGTTTCTATAACTGGTGTAACCGCAAAAAATGGTCACTTTTTATCATCATTACTAGCTG
GTTTTGGTTTTATACTGCAAGCAGAACTTTGATAAATTCATTTGAAGCTTCTCTTACAAC
AATCGCTTTAAGTTTCTTTCCTTGGAACAAATTTGATGAAAATACTGGATTTTTGTGGAT
CACTGCTTTATTGTCATTTATTCGACCAACATCGATTGTCACATGGTTACCTTTATGTAT
TTATCACGTAAAAAAATCAAAATATCCAGTTTGGGAATTGTTGATTAAACGCTATTTGTT
TATTGGACTTGTAACTGGAGGAGCATTAATTGCACTAGATTCTTTCTTCCATGGATCATT
CATAGTTACACCATATGAGTTCATTAAAATCAACGTTTTTGAAGGAATAGCTAGTTTTTA
TGGTACTCATCCATTTTACTGGTATTTTAGCACAGGACTGCCTGCTATTCTTGGTATTGG
AATAGTTCCATTCTATTTATCAATTTTTACAACAATCAAACGATCATGGGATCAATCGAC
AATTGCAATTATGACTTCAATTATATTGACCATTTTCATGTACTCTCTACTGCCACACAA
AGAATTTAGATTTTTGCTTCAAATACTGCCACTTTGTCTTTACTGTATTACACAATTCCT
GTCAGAATGGAGTAGAACAAAGTCATCACTCGTCATTTGGTTTGTAGCTATAGTCATTTT
TATAAGCAATGCAGTGCCAGCTGGATATCTCGGTTTCGTTCATCAACAAGGAACAATAAA
AGTTATGGATCAAGTTTCTTCAATTGCAAACAACTATAAAACACAAGACGGACATCCAGC
AAAAATATTTTTCATGATGCCATGTCATTCAACGCCTTTTTATTCACACGTCCATAAAAA
CATTACAATGAGATTCCTCACTTGTGAGCCTAATCTTAACAATCAGTTGAATTATGTAGA
TGAAGCTGATAAATTTTATGAAGCTCCAATGAAATGGATTCGAAGTCATTTACCGGTACA
TCCAGTGAATGCATTGCCAACTCACGTTGTGGTATTCGACACTCTAGTACCAATGATCAG
TGATTTTCTTTCACTCTATAAACCAATCGAAATTTTCTTCCATGCTGATCATCTCGTCTC
ACAACGTGCAGGACATAACGTTTTAATTTATGAGCGTAATGAACAAGAAGTCAAGAAAAA
GGAAGAGGAGAAAGTTATTAAGCAAAAAGATCAAAAAGTTCCGGATGAGCTTTAA

>g11859.t7 Gene=g11859 Length=490
MNIGKVWKLVIVWSSSNYGHLTWEWIQGIRSYFYPTLFAAIYKVLDILKIDSRVFLILLP
RIFQALISTYADYRFYNWCNRKKWSLFIIITSWFWFYTASRTLINSFEASLTTIALSFFP
WNKFDENTGFLWITALLSFIRPTSIVTWLPLCIYHVKKSKYPVWELLIKRYLFIGLVTGG
ALIALDSFFHGSFIVTPYEFIKINVFEGIASFYGTHPFYWYFSTGLPAILGIGIVPFYLS
IFTTIKRSWDQSTIAIMTSIILTIFMYSLLPHKEFRFLLQILPLCLYCITQFLSEWSRTK
SSLVIWFVAIVIFISNAVPAGYLGFVHQQGTIKVMDQVSSIANNYKTQDGHPAKIFFMMP
CHSTPFYSHVHKNITMRFLTCEPNLNNQLNYVDEADKFYEAPMKWIRSHLPVHPVNALPT
HVVVFDTLVPMISDFLSLYKPIEIFFHADHLVSQRAGHNVLIYERNEQEVKKKEEEKVIK
QKDQKVPDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11859.t7 Coils Coil Coil 463 485 -
2 g11859.t7 PANTHER PTHR22760 GLYCOSYLTRANSFERASE 17 464 7.9E-111
3 g11859.t7 PANTHER PTHR22760:SF4 GPI MANNOSYLTRANSFERASE 3 17 464 7.9E-111
1 g11859.t7 Pfam PF03901 Alg9-like mannosyltransferase family 13 371 1.0E-88
17 g11859.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 53 -
27 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 73 -
14 g11859.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 84 -
23 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 104 -
15 g11859.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 105 128 -
25 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
13 g11859.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 152 170 -
26 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 198 -
19 g11859.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 199 217 -
24 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 241 -
11 g11859.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 242 252 -
22 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 253 271 -
16 g11859.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 272 276 -
20 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 277 296 -
12 g11859.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 297 302 -
21 g11859.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 303 325 -
18 g11859.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 326 490 -
6 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 103 -
9 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
7 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 172 194 -
8 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 219 241 -
4 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 253 270 -
5 g11859.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 304 326 -

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

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.

Raw TPM values