General information for g5080.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative GILT-like protein 1.
Parent gene
- The parent gene g5080 is located on chr_2: 6807748..6808384 (- 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_2 | g5080 | g5080.t6 | TTS | g5080.t6 | 6806720 | 6806720 |
| chr_2 | g5080 | g5080.t6 | isoform | g5080.t6 | 6806957 | 6808384 |
| chr_2 | g5080 | g5080.t6 | exon | g5080.t6.exon1 | 6806957 | 6807215 |
| chr_2 | g5080 | g5080.t6 | cds | g5080.t6.CDS1 | 6806957 | 6807215 |
| chr_2 | g5080 | g5080.t6 | exon | g5080.t6.exon2 | 6807714 | 6807843 |
| chr_2 | g5080 | g5080.t6 | cds | g5080.t6.CDS2 | 6807714 | 6807843 |
| chr_2 | g5080 | g5080.t6 | exon | g5080.t6.exon3 | 6807908 | 6807934 |
| chr_2 | g5080 | g5080.t6 | cds | g5080.t6.CDS3 | 6807908 | 6807934 |
| chr_2 | g5080 | g5080.t6 | exon | g5080.t6.exon4 | 6808004 | 6808190 |
| chr_2 | g5080 | g5080.t6 | cds | g5080.t6.CDS4 | 6808004 | 6808190 |
| chr_2 | g5080 | g5080.t6 | exon | g5080.t6.exon5 | 6808268 | 6808384 |
| chr_2 | g5080 | g5080.t6 | cds | g5080.t6.CDS5 | 6808268 | 6808384 |
| chr_2 | g5080 | g5080.t6 | TSS | g5080.t6 | 6808536 | 6808536 |
Sequences
>g5080.t6 Gene=g5080 Length=720
ATGAAGCGATTTAGTGGACAAGCTAGATTTAAAATAATTGCTGTGGTTTCAATATTACTC
ATCTTTTACTATGCTTATAGAAGTTTCACAGATTATAATAATCGTTTAATTCATGAGGAT
CAATTGGAATTTGCGCGTACGAAAGGTACACCAATCATTGTAGCTGTTTATTATGAGGCA
CTATGTCCTGACAGCAAAAATTTTATTGTAAAACAACTCAAATCGGCCTATTCAAAGCTT
CCAAATCTCATAGAAATTGAATTTTTCCCTTATGGCAAAGCTTCGACTAATGTTCAACCT
GATGGTTCTCTTTCATTTCAATGTCAACATGGAGCGAGAGAATGCGAGGGAAATATTATT
CATTGTTGTGCAGTCGAATCAATTCATGATACTGAAATGAGACTGAATTTTGTTGCATGC
ATGATTCGTGACAATTCGAATCCGCAAGAAGCTTTTCANNNATGTACGAAAGAATTTGCA
ATTGATGTTAGCACAGTAGAAACAATTCAAAAATGTTATAATAGTCTTCATGGTAAAGAA
CTACTTAAAATAGCAGGAGAAGCAACTCACAATTTAAACCCATCTGTTTCATTCATTCCC
ACAATTACACTCGATGGTCAACAACGACGACAAGCGACAATTTTACGCGATTTATTTTCA
GAAATATGTGCTGTTCTTGCAGAATCGGGACTTACGCCTAAGGCTTGCGAAAGCATATAG
>g5080.t6 Gene=g5080 Length=239
MKRFSGQARFKIIAVVSILLIFYYAYRSFTDYNNRLIHEDQLEFARTKGTPIIVAVYYEA
LCPDSKNFIVKQLKSAYSKLPNLIEIEFFPYGKASTNVQPDGSLSFQCQHGARECEGNII
HCCAVESIHDTEMRLNFVACMIRDNSNPQEAFXXCTKEFAIDVSTVETIQKCYNSLHGKE
LLKIAGEATHNLNPSVSFIPTITLDGQQRRQATILRDLFSEICAVLAESGLTPKACESI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5080.t6 | PANTHER | PTHR13234:SF59 | GAMMA-INTERFERON-INDUCIBLE LYSOSOMAL THIOL REDUCTASE-LIKE PROTEIN | 11 | 236 | 2.0E-71 |
| 3 | g5080.t6 | PANTHER | PTHR13234 | GAMMA-INTERFERON INDUCIBLE LYSOSOMAL THIOL REDUCTASE GILT | 11 | 236 | 2.0E-71 |
| 1 | g5080.t6 | Pfam | PF03227 | Gamma interferon inducible lysosomal thiol reductase (GILT) | 54 | 158 | 3.0E-32 |
| 5 | g5080.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 7 | g5080.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
| 6 | g5080.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 239 | - |
| 4 | g5080.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5080/g5080.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5080.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K08059 (interferon, gamma-inducible protein 30)
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.
