Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Fringe glycosyltransferase.

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 g10022 g10022.t5 isoform g10022.t5 6765077 6766476
chr_1 g10022 g10022.t5 exon g10022.t5.exon1 6765077 6765081
chr_1 g10022 g10022.t5 exon g10022.t5.exon2 6765283 6765597
chr_1 g10022 g10022.t5 cds g10022.t5.CDS1 6765289 6765597
chr_1 g10022 g10022.t5 exon g10022.t5.exon3 6765662 6766476
chr_1 g10022 g10022.t5 cds g10022.t5.CDS2 6765662 6765817
chr_1 g10022 g10022.t5 TTS g10022.t5 6766471 6766471
chr_1 g10022 g10022.t5 TSS g10022.t5 NA NA

Sequences

>g10022.t5 Gene=g10022 Length=1135
ATGCGGCGATAATGAGCTTAGAGCAGACAAAAAAATATTCCAAAGAGGAGGAAAAACGTC
GCGAGAATGAAAAGGTGAAATTTTGGTTCGCAACGGGAGGAGCCGGTTTTTGTATAAGTC
GTGCATTAGCAATAAAAATGATGCCACTAACAAGCAAAGGCAAATTTATAGCAATTGGAG
ATGGAATAAGATTTCCAGACGATGTAACGCTTGGTTTTATTATTGAGTACCTTCTGAAAG
TTCCTTTAACCGTGGTCAATCCCTTTCATTCACATCTTGAACGTATGGATCACATTGACA
CTGAAATTTTTCGTGATCAGATCTCATTCAGCTATGCGCACATAAAAGATGATTGGAACG
TTGTTAAAGTCGTCAATGGATTCGATACGACGAAAGATCCATACCGATTTTATTCATTGC
ATTGTTACCTTTTCCCACACTTTGAGATGTGCAAAAGTCTTCGTCTTCGTCGATAGATCG
ATGTAGCATCCCATCATGTTGTTGCTGTTGTTTTATTTGCCATTAAAGATGAATTTATAT
ATTTTTATTTTATTACAATCAATGCGATTATCTGTGATCAACTGCAGTCTCTCGACTGCA
ACAACAGCGTTGCTCAGCACGCTAAGTGAATCTTCCTCAATAGCAATAGATTGATAGCAT
TAAGTATAGGTTAATTAAGTGAGAAATGCGAAGTGCTTGAGCTCTCACTGAAATTAGAAT
CTTTTAAAACAAACGTGGCACAATGTGATTGGATTAAATTTATTTGATTGCATGCTTGAT
TTATGATTATTCTCTGATCCGATTATTGCCATGTTTGATTATCTTTATGTACTATTTTTA
TTCTGAAATATTAAATTTATTTTTCACTCACTCAAAAAATATGAAAATTTACCGCGCCTC
GCGAGCTTTAATTTATGAGCGAAAATTTTTTGAGCATGTTAGCTTCGCATGTATGCAAAA
TAAAATATAATAATAGTAATGAACTCAAGTCTCATCTTTGTAAGAGAATAAGAAAGAAAC
TGAGGTCATGTCATTTTATAGCTGTGATTGTAAATAACCGTGAATCATGCGGAAAGTTAA
AATGATATTTTGGATAAGCGAAAAGGAAATAAAAAATCTTTTTTACTAAGAATTA

>g10022.t5 Gene=g10022 Length=154
MSLEQTKKYSKEEEKRRENEKVKFWFATGGAGFCISRALAIKMMPLTSKGKFIAIGDGIR
FPDDVTLGFIIEYLLKVPLTVVNPFHSHLERMDHIDTEIFRDQISFSYAHIKDDWNVVKV
VNGFDTTKDPYRFYSLHCYLFPHFEMCKSLRLRR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g10022.t5 Gene3D G3DSA:3.90.550.50 - 1 152 3.5E-60
2 g10022.t5 PANTHER PTHR10811 FRINGE-RELATED 18 148 2.4E-58
3 g10022.t5 PANTHER PTHR10811:SF103 FRINGE GLYCOSYLTRANSFERASE 18 148 2.4E-58
1 g10022.t5 Pfam PF02434 Fringe-like 11 132 5.8E-42
7 g10022.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 23 -
8 g10022.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 41 -
6 g10022.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 42 154 -
4 g10022.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 41 -

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:0016020 membrane CC
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