General information for g5534.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5534 is located on chr_2: 10128055..10128867 (- 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 | g5534 | g5534.t17 | TTS | g5534.t17 | 10126405 | 10126405 |
| chr_2 | g5534 | g5534.t17 | isoform | g5534.t17 | 10126849 | 10128344 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon1 | 10126849 | 10126862 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon2 | 10126920 | 10126955 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon3 | 10127012 | 10127232 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon4 | 10127302 | 10127353 |
| chr_2 | g5534 | g5534.t17 | cds | g5534.t17.CDS1 | 10127348 | 10127353 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon5 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t17 | cds | g5534.t17.CDS2 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon6 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t17 | cds | g5534.t17.CDS3 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon7 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t17 | cds | g5534.t17.CDS4 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t17 | exon | g5534.t17.exon8 | 10128130 | 10128344 |
| chr_2 | g5534 | g5534.t17 | cds | g5534.t17.CDS5 | 10128130 | 10128223 |
| chr_2 | g5534 | g5534.t17 | TSS | g5534.t17 | 10128343 | 10128343 |
Sequences
>g5534.t17 Gene=g5534 Length=987
CAGTGATAGATAGAAGTCTCAAGAAGAGAGTAATACCTAATTCTCATCAGTTTCCTCGAT
CATGTAAATTTAGTTCTAAAATTCACATAAAATTGTAATTTTTTATATTTCTAGTGTCGA
AATGTTCGTGATTAAAATGAAATTTTTAACTTTTAATCTAAATATTTTAATCATCATTGT
TCTGTCAAATTTAATATTGATTGAGTCACTCGAAGAGGGAAGTCCTTGTACGAGTTTTGA
TAATTCTCCAGGAGTTTGTAAAGTTTTGTCACAATGCAACTGGGCAGTTGATAAGATTAA
ATCTAAAGAAATTGCAATTGGACAATTGATTAGATGTGGTTTTAAAAATCGAGATGTGAT
TATTTGTTGCAAACATAATGTTGCTCCGCCATTAGAATTAGTTGTGAACACTAAAAGTCC
AGCATCTACAACAGTGTATGGTGAAGACAGACCTCCAGTTTTCGTAACGTTTCAATCACA
AAGAAAATCAATACAGGCATGTGAACAAATTAAAAAAATTGTTCCAATTGGTGTTCAATT
CAATATAATTGGCGGTGAACAGGCTGAAAAAGGAGAATTTCCGCATCAAGTTGTGTTAGG
ATATCCCGATGAATTAGACCCAAATAAAATTTCATACGATTGTGGTGGAAGTTTAATATC
AAAGTTTTAAAAATCATTTACAGCTCATTGCGTCAATAACCGACAACGACAACCAAATTT
TACTTGGCAAGACATCCTTAAATGATGATGATGAACTTGATCCAATTTTAATACCAGTTA
AAAAAATAATAATTCATTCCAATTATACATCTAGACGAAAATATGACGATATTGCTTTGA
TTGAATTAGAACATAACGTAGAAAAATATAACTATTATGTTAAACCAGCTTGCCTTTATA
CAAAGCATACAATCTTAACTGAAATTGCAATCATCACAGGATTTGGCATTGTTAATCAAG
AAACAAGGAGAAAATCTGATTGGCTAA
>g5534.t17 Gene=g5534 Length=182
MFVIKMKFLTFNLNILIIIVLSNLILIESLEEGSPCTSFDNSPGVCKVLSQCNWAVDKIK
SKEIAIGQLIRCGFKNRDVIICCKHNVAPPLELVVNTKSPASTTVYGEDRPPVFVTFQSQ
RKSIQACEQIKKIVPIGVQFNIIGGEQAEKGEFPHQVVLGYPDELDPNKISYDCGGSLIS
KF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5534.t17 | Gene3D | G3DSA:2.40.10.10 | - | 142 | 182 | 6.8E-7 |
| 1 | g5534.t17 | PANTHER | PTHR24260:SF107 | EG:BACR7A4.3 PROTEIN-RELATED | 16 | 181 | 1.3E-12 |
| 2 | g5534.t17 | PANTHER | PTHR24260 | - | 16 | 181 | 1.3E-12 |
| 5 | g5534.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 8 | - |
| 7 | g5534.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 27 | - |
| 6 | g5534.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 182 | - |
| 3 | g5534.t17 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 123 | 181 | 2.74E-8 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5534/g5534.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5534.t17.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. There were no conditions that were differentially expressed