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.t4 isoform g11859.t4 18795625 18797861
chr_1 g11859 g11859.t4 exon g11859.t4.exon1 18795625 18797216
chr_1 g11859 g11859.t4 cds g11859.t4.CDS1 18796120 18797216
chr_1 g11859 g11859.t4 exon g11859.t4.exon2 18797265 18797594
chr_1 g11859 g11859.t4 cds g11859.t4.CDS2 18797265 18797271
chr_1 g11859 g11859.t4 exon g11859.t4.exon3 18797734 18797861
chr_1 g11859 g11859.t4 TSS g11859.t4 18797889 18797889
chr_1 g11859 g11859.t4 TTS g11859.t4 NA NA

Sequences

>g11859.t4 Gene=g11859 Length=2050
ATGTCAACAATTTTTGTGATTTTTCTATTATTATTTGTAAGAATCGCGTCAGTTTTTCTC
GTACAAACTTTCTTTAGTCCTGATGAATATTGGCAAAGTGTGGAAGTTAGTCATCGTATG
GTCTTCAATTATGGACATCTTACATGGGAATGGATTCAAGGAATTCGAAGTTATTTTTAC
CCGACGCTCTTTGCAGCCATTTACAAAGTTCTTGATATTTTAAAAATAGACTCACGCGTC
TTTTTGATTCTCCTACCGAGAATATTTCAAGCTCTCATCTCAACCTACGCAGATTATCGT
TTCTATAACTGGTGTAACCGCAAAAAATGGTCACTTTTTATCATCATTACTAGCTGGTTT
TGGTTTTATACTGCAAGCAGAACTTTGATAAATTCATTTGAAGCTTCTCTTACAACAATC
GCTTTAAGTTTCTTTCCTTGGAACAAATTTGATGGTAAAAAATACTGGATTTTTGTGGAT
CACTGCTTTATTGTCATTTATTCGACCAACATCGATTGTCACATGGTTACCTTTATGTAT
TTATCACGTAAAAAAATCAAAATATCCAGTTTGGGAATTGTTGATTAAACGCTATTTGTT
TATTGGACTTGTAACTGGAGGAGCATTAATTGCACTAGATTCTTTCTTCCATGGATCATT
CATAGTTACACCATATGAGTTCATTAAAATCAACGTTTTTGAAGGAATAGCTAGTTTTTA
TGGTACTCATCCATTTTACTGGTATTTTAGCACAGGACTGCCTGCTATTCTTGGTATTGG
AATAGTTCCATTCTATTTATCAATTTTTACAACAATCAAACGATCATGGGATCAATCGAC
AATTGCAATTATGACTTCAATTATATTGACCATTTTCATGTACTCTCTACTGCCACACAA
AGAATTTAGATTTTTGCTTCAAATACTGCCACTTTGTCTTTACTGTATTACACAATTCCT
GTCAGAATGGAGTAGAACAAAGTCATCACTCGTCATTTGGTTTGTAGCTATAGTCATTTT
TATAAGCAATGCAGTGCCAGCTGGATATCTCGGTTTCGTTCATCAACAAGGAACAATAAA
AGTTATGGATCAAGTTTCTTCAATTGCAAACAACTATAAAACACAAGACGGACATCCAGC
AAAAATATTTTTCATGATGCCATGTCATTCAACGCCTTTTTATTCACACGTCCATAAAAA
CATTACAATGAGATTCCTCACTTGTGAGCCTAATCTTAACAATCAGTTGAATTATGTAGA
TGAAGCTGATAAATTTTATGAAGCTCCAATGAAATGGATTCGAAGTCATTTACCGGTACA
TCCAGTGAATGCATTGCCAACTCACGTTGTGGTATTCGACACTCTAGTACCAATGATCAG
TGATTTTCTTTCACTCTATAAACCAATCGAAATTTTCTTCCATGCTGATCATCTCGTCTC
ACAACGTGCAGGACATAACGTTTTAATTTATGAGCGTAATGAACAAGAAGTCAAGAAAAA
GGAAGAGGAGAAAGTTATTAAGCAAAAAGATCAAAAAGTTCCGGATGAGCTTTAAAAGAT
GATGACTTAATTATTTTCGCGTAACAGTGTGTCTTGATTAGCAATATATTTTCAATCTCT
AATTGCTATCATTTAAAAACCATAAACACATACATACAGGTAAAATAAATAAAATTAAGA
AAAAAAAACACAAAGAATCAATTTGACGAAAAAAAATGTTGCAATACGAAAAATTAGTGA
ATTTTTATGCCCTTTCTAGCTAATTGAAATTTCATATTTTGCTTAAATTTTAAATTGAAA
AAAATATTTTAAATTTTAATATTTTATTTTTTGATCCTTAAATCATAAAATCATTTATTT
GAAAATGTAGTAAAAAAACTTTAGTTTATTTGACAAGAAATAAAAAGAAACGATTTAATT
ATAAGAAAGATTTATAACCATGTCATGCCATCTTATTCACAGTCATTCACAAATTATCAA
ATTTATTTTTTTCCAGATGTAAGTCTTCAATCTGATTTATTATAGCATCATTTTATTCGA
TCTACACAGT

>g11859.t4 Gene=g11859 Length=367
MVKNTGFLWITALLSFIRPTSIVTWLPLCIYHVKKSKYPVWELLIKRYLFIGLVTGGALI
ALDSFFHGSFIVTPYEFIKINVFEGIASFYGTHPFYWYFSTGLPAILGIGIVPFYLSIFT
TIKRSWDQSTIAIMTSIILTIFMYSLLPHKEFRFLLQILPLCLYCITQFLSEWSRTKSSL
VIWFVAIVIFISNAVPAGYLGFVHQQGTIKVMDQVSSIANNYKTQDGHPAKIFFMMPCHS
TPFYSHVHKNITMRFLTCEPNLNNQLNYVDEADKFYEAPMKWIRSHLPVHPVNALPTHVV
VFDTLVPMISDFLSLYKPIEIFFHADHLVSQRAGHNVLIYERNEQEVKKKEEEKVIKQKD
QKVPDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11859.t4 Coils Coil Coil 340 362 -
2 g11859.t4 PANTHER PTHR22760 GLYCOSYLTRANSFERASE 8 341 1.7E-72
3 g11859.t4 PANTHER PTHR22760:SF4 GPI MANNOSYLTRANSFERASE 3 8 341 1.7E-72
1 g11859.t4 Pfam PF03901 Alg9-like mannosyltransferase family 5 248 6.2E-57
15 g11859.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
13 g11859.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 29 47 -
23 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 48 75 -
16 g11859.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 76 94 -
19 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 118 -
12 g11859.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 119 129 -
20 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 148 -
14 g11859.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 153 -
22 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 173 -
11 g11859.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 174 179 -
21 g11859.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
17 g11859.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 203 367 -
6 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
5 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 49 71 -
7 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 118 -
8 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
9 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 171 -
4 g11859.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 181 203 -

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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