General information for g5573.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transmembrane protein 242.
Parent gene
- The parent gene g5573 is located on chr_2: 10348952..10349687 (- 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 | g5573 | g5573.t13 | isoform | g5573.t13 | 10348313 | 10348952 |
| chr_2 | g5573 | g5573.t13 | exon | g5573.t13.exon1 | 10348313 | 10348817 |
| chr_2 | g5573 | g5573.t13 | TTS | g5573.t13 | 10348411 | 10348411 |
| chr_2 | g5573 | g5573.t13 | cds | g5573.t13.CDS1 | 10348480 | 10348817 |
| chr_2 | g5573 | g5573.t13 | exon | g5573.t13.exon2 | 10348871 | 10348952 |
| chr_2 | g5573 | g5573.t13 | cds | g5573.t13.CDS2 | 10348871 | 10348952 |
| chr_2 | g5573 | g5573.t13 | TSS | g5573.t13 | 10349007 | 10349007 |
Sequences
>g5573.t13 Gene=g5573 Length=587
ATGAGCGAAAATACGCGAATGACAATTGATGAAGCTAGAAAATATAAATTCAAGGCTGCA
GCTTTTCTTATTGGTGTTGCAGGCATTTCTGCGGCTATTGGGTTTTCGAGAACACTTGCA
ATGGCTAAGAAAAAAGACACAATGTATTTTACAAAAGGAATGCAAGAATCACCAGATTTA
GCAGGAGTTCAATTGGCAATGAAGGCTTTAGGCTACGGAACGTTATATGCAGTAATAGGC
ACAGGATCATTATTTTATGGAATATGGAAATTATCGGGAGCAAAAAATCTCGAAGAGTTC
AGAATCAAATGTGGCAATATTCTCCCACGGATTCCTAAAAACGAAGTACCAACTTCAAGA
ACTGAATTTGAAGGATTGAATGATTTAATGACTTATTTATCTACTTGGAAAAAAGATTAG
AAATAGAAAATAATATCTTAGACATATTGTAACGACTTTGAAAAATTCAAATAAAAAAAT
TGTAAAATTATTGAGATGCGTTTCCTTTAAAAATTGTGTCTCAAAACAACAAAGATTTTA
AAATTGCCGAATAATTATTTTTTGTGAGAAATATCAAATTTAAACAT
>g5573.t13 Gene=g5573 Length=139
MSENTRMTIDEARKYKFKAAAFLIGVAGISAAIGFSRTLAMAKKKDTMYFTKGMQESPDL
AGVQLAMKALGYGTLYAVIGTGSLFYGIWKLSGAKNLEEFRIKCGNILPRIPKNEVPTSR
TEFEGLNDLMTYLSTWKKD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5573.t13 | PANTHER | PTHR13141 | TRANSMEMBRANE PROTEIN 242 | 3 | 138 | 1.8E-41 |
| 1 | g5573.t13 | Pfam | PF07096 | Protein of unknown function (DUF1358) | 4 | 111 | 1.3E-37 |
| 5 | g5573.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 19 | - |
| 9 | g5573.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 40 | - |
| 7 | g5573.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 41 | 68 | - |
| 8 | g5573.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 89 | - |
| 6 | g5573.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 90 | 139 | - |
| 3 | g5573.t13 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 19 | 41 | - |
| 4 | g5573.t13 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 91 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5573/g5573.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5573.t13.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
