General information for g5534.t13
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.t13 | TTS | g5534.t13 | 10126405 | 10126405 |
| chr_2 | g5534 | g5534.t13 | isoform | g5534.t13 | 10126447 | 10128208 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon1 | 10126447 | 10126628 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon2 | 10126699 | 10126862 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon3 | 10126920 | 10126955 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon4 | 10127012 | 10127232 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS1 | 10127208 | 10127232 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon5 | 10127297 | 10127346 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS2 | 10127297 | 10127346 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon6 | 10127478 | 10127566 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS3 | 10127478 | 10127566 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon7 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS4 | 10127629 | 10127759 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon8 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS5 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t13 | exon | g5534.t13.exon9 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t13 | cds | g5534.t13.CDS6 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t13 | TSS | g5534.t13 | 10128343 | 10128343 |
Sequences
>g5534.t13 Gene=g5534 Length=1178
ATGAAATTTTTAACTTTTAATCTAAATATTTTAATCATCATTGTTCTGTCAAATTTAATA
TTGATTGAGTCACTCGAAGAGGGAAGTCCTTGTACGAGTTTTGATAATTCTCCAGGAGTT
TGTAAAGTTTTGTCACAATGCAACTGGGCAGTTGATAAGATTAAATCTAAAGAAATTGCA
ATTGGACAATTGATTAGATGTGGTTTTAAAAATCGAGATGTGATTATTTGTTGCAAACAT
AATGTTGCTCCGCCATTAGAATTAGTTGTGAACACTAAAAGTCCAGCATCTACAACAGTG
TATGGTGAAGACAGACCTCCAGTTTTCGTAACGTTTCAATCACAAAGAAAATCAATACAG
GCATGTGAACAAATTAAAAAAATTGTTCCAATTGGTGTTCAATTCAATATAATTGGCGGT
GAACAGGCTGAAAAAGAATTTCCGCATCAAGTTGTGTTAGGATATCCCGATGAATTAGAC
CCAAATAAAATTTCATACGATTGTGGTGGAAGTTTAATATCAAAGAATCATTTACAGCTC
ATTGCGTCAATAACCGACAACGACAACCAAGTGTTATTTTACTTGGCAAGACATCCTTAA
ATGATGATGATGAACTTGATCCAATTTTAATACCAGTTAAAAAAATAATAATTCATTCCA
ATTATACATCTAGACGAAAATATGACGATATTGCTTTGATTGAATTAGAACATAACGTAG
AAAAATATAACTATTATGTTAAACCAGCTTGCCTTTATACAAAGCATACAATCTTAACTG
AAATTGCAATCATCACAGGATTTGGCATTGTTAATCAAGAAACAAGGAGAAAATCTGATT
GGCTAATGAAAGCAGATGTAACTGAAGTGCCGTTGACTGATTGTAGAGAAAAATATGCAA
CGACTGGTTTATCAAGAATTCCAGATAATTTAAGACAGACACAAATGTGCGCTACTGGTA
TAAATAGTGCCGGCACAACTATTGATGCATGTCAAGGTGATAGCGGAGGTCCGATTCAAA
TAAAGGAGTTATACAAGGGAGAAAAATATTATACAGTTGTGGGAGTGACAAGTTTTGGAG
CAAGCTGTGGAAGTCAAATTCCAGGTGTATATACTCGAGTATCTGAATACTTAGATTGGA
TTGAACCAATTGTTTGGCCTAGTAATGTAGTCATTTAA
>g5534.t13 Gene=g5534 Length=199
MKFLTFNLNILIIIVLSNLILIESLEEGSPCTSFDNSPGVCKVLSQCNWAVDKIKSKEIA
IGQLIRCGFKNRDVIICCKHNVAPPLELVVNTKSPASTTVYGEDRPPVFVTFQSQRKSIQ
ACEQIKKIVPIGVQFNIIGGEQAEKEFPHQVVLGYPDELDPNKISYDCGGSLISKNHLQL
IASITDNDNQVLFYLARHP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5534.t13 | Gene3D | G3DSA:2.40.10.10 | - | 137 | 189 | 3.2E-5 |
| 5 | g5534.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 6 | g5534.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 4 | g5534.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 199 | - |
| 1 | g5534.t13 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 118 | 177 | 5.53E-6 |
| 2 | g5534.t13 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5534/g5534.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5534.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. There were no conditions that were differentially expressed