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.t6 isoform g11859.t6 18795625 18797861
chr_1 g11859 g11859.t6 exon g11859.t6.exon1 18795625 18797216
chr_1 g11859 g11859.t6 cds g11859.t6.CDS1 18796120 18797216
chr_1 g11859 g11859.t6 exon g11859.t6.exon2 18797269 18797493
chr_1 g11859 g11859.t6 cds g11859.t6.CDS2 18797269 18797493
chr_1 g11859 g11859.t6 exon g11859.t6.exon3 18797554 18797594
chr_1 g11859 g11859.t6 cds g11859.t6.CDS3 18797554 18797594
chr_1 g11859 g11859.t6 exon g11859.t6.exon4 18797734 18797861
chr_1 g11859 g11859.t6 cds g11859.t6.CDS4 18797734 18797861
chr_1 g11859 g11859.t6 TSS g11859.t6 18797889 18797889
chr_1 g11859 g11859.t6 TTS g11859.t6 NA NA

Sequences

>g11859.t6 Gene=g11859 Length=1986
ATGTCAACAATTTTTGTGATTTTTCTATTATTATTTGTAAGAATCGCGTCAGTTTTTCTC
GTACAAACTTTCTTTAGTCCTGATGAATATTGGCAAAGTGTGGAAGTTAGTCATCGTATG
GTCTTCAATTATGGACATCTTACATGGGAATGGATTCAAGGAATTCGAAACTCACGCGTC
TTTTTGATTCTCCTACCGAGAATATTTCAAGCTCTCATCTCAACCTACGCAGATTATCGT
TTCTATAACTGGTGTAACCGCAAAAAATGGTCACTTTTTATCATCATTACTAGCTGGTTT
TGGTTTTATACTGCAAGCAGAACTTTGATAAATTCATTTGAAGCTTCTCTTACAACAATC
GCTTTAAGTTTCTTTCCTTGGAACAAATTTGATGAAAATACTGGATTTTTGTGGATCACT
GCTTTATTGTCATTTATTCGACCAACATCGATTGTCACATGGTTACCTTTATGTATTTAT
CACGTAAAAAAATCAAAATATCCAGTTTGGGAATTGTTGATTAAACGCTATTTGTTTATT
GGACTTGTAACTGGAGGAGCATTAATTGCACTAGATTCTTTCTTCCATGGATCATTCATA
GTTACACCATATGAGTTCATTAAAATCAACGTTTTTGAAGGAATAGCTAGTTTTTATGGT
ACTCATCCATTTTACTGGTATTTTAGCACAGGACTGCCTGCTATTCTTGGTATTGGAATA
GTTCCATTCTATTTATCAATTTTTACAACAATCAAACGATCATGGGATCAATCGACAATT
GCAATTATGACTTCAATTATATTGACCATTTTCATGTACTCTCTACTGCCACACAAAGAA
TTTAGATTTTTGCTTCAAATACTGCCACTTTGTCTTTACTGTATTACACAATTCCTGTCA
GAATGGAGTAGAACAAAGTCATCACTCGTCATTTGGTTTGTAGCTATAGTCATTTTTATA
AGCAATGCAGTGCCAGCTGGATATCTCGGTTTCGTTCATCAACAAGGAACAATAAAAGTT
ATGGATCAAGTTTCTTCAATTGCAAACAACTATAAAACACAAGACGGACATCCAGCAAAA
ATATTTTTCATGATGCCATGTCATTCAACGCCTTTTTATTCACACGTCCATAAAAACATT
ACAATGAGATTCCTCACTTGTGAGCCTAATCTTAACAATCAGTTGAATTATGTAGATGAA
GCTGATAAATTTTATGAAGCTCCAATGAAATGGATTCGAAGTCATTTACCGGTACATCCA
GTGAATGCATTGCCAACTCACGTTGTGGTATTCGACACTCTAGTACCAATGATCAGTGAT
TTTCTTTCACTCTATAAACCAATCGAAATTTTCTTCCATGCTGATCATCTCGTCTCACAA
CGTGCAGGACATAACGTTTTAATTTATGAGCGTAATGAACAAGAAGTCAAGAAAAAGGAA
GAGGAGAAAGTTATTAAGCAAAAAGATCAAAAAGTTCCGGATGAGCTTTAAAAGATGATG
ACTTAATTATTTTCGCGTAACAGTGTGTCTTGATTAGCAATATATTTTCAATCTCTAATT
GCTATCATTTAAAAACCATAAACACATACATACAGGTAAAATAAATAAAATTAAGAAAAA
AAAACACAAAGAATCAATTTGACGAAAAAAAATGTTGCAATACGAAAAATTAGTGAATTT
TTATGCCCTTTCTAGCTAATTGAAATTTCATATTTTGCTTAAATTTTAAATTGAAAAAAA
TATTTTAAATTTTAATATTTTATTTTTTGATCCTTAAATCATAAAATCATTTATTTGAAA
ATGTAGTAAAAAAACTTTAGTTTATTTGACAAGAAATAAAAAGAAACGATTTAATTATAA
GAAAGATTTATAACCATGTCATGCCATCTTATTCACAGTCATTCACAAATTATCAAATTT
ATTTTTTTCCAGATGTAAGTCTTCAATCTGATTTATTATAGCATCATTTTATTCGATCTA
CACAGT

>g11859.t6 Gene=g11859 Length=496
MSTIFVIFLLLFVRIASVFLVQTFFSPDEYWQSVEVSHRMVFNYGHLTWEWIQGIRNSRV
FLILLPRIFQALISTYADYRFYNWCNRKKWSLFIIITSWFWFYTASRTLINSFEASLTTI
ALSFFPWNKFDENTGFLWITALLSFIRPTSIVTWLPLCIYHVKKSKYPVWELLIKRYLFI
GLVTGGALIALDSFFHGSFIVTPYEFIKINVFEGIASFYGTHPFYWYFSTGLPAILGIGI
VPFYLSIFTTIKRSWDQSTIAIMTSIILTIFMYSLLPHKEFRFLLQILPLCLYCITQFLS
EWSRTKSSLVIWFVAIVIFISNAVPAGYLGFVHQQGTIKVMDQVSSIANNYKTQDGHPAK
IFFMMPCHSTPFYSHVHKNITMRFLTCEPNLNNQLNYVDEADKFYEAPMKWIRSHLPVHP
VNALPTHVVVFDTLVPMISDFLSLYKPIEIFFHADHLVSQRAGHNVLIYERNEQEVKKKE
EEKVIKQKDQKVPDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11859.t6 Coils Coil Coil 469 491 -
2 g11859.t6 PANTHER PTHR22760 GLYCOSYLTRANSFERASE 8 470 1.0E-115
3 g11859.t6 PANTHER PTHR22760:SF4 GPI MANNOSYLTRANSFERASE 3 8 470 1.0E-115
1 g11859.t6 Pfam PF03901 Alg9-like mannosyltransferase family 6 377 4.9E-87
22 g11859.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
23 g11859.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
24 g11859.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 13 -
33 g11859.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 20 -
20 g11859.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 59 -
27 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 79 -
13 g11859.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 80 90 -
28 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 91 110 -
19 g11859.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 134 -
32 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 157 -
15 g11859.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 158 176 -
30 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 177 204 -
18 g11859.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 205 223 -
31 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 224 247 -
16 g11859.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 248 258 -
25 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 277 -
17 g11859.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 278 282 -
26 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 283 302 -
14 g11859.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 303 308 -
29 g11859.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 309 331 -
21 g11859.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 332 496 -
11 g11859.t6 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -
6 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -
4 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 109 -
10 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 157 -
9 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 200 -
5 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -
8 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 259 276 -
7 g11859.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 310 332 -

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