General information for g17702.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17702 is located on HiC_scaffold_86: 4233..5288 (- 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_86 | g17702 | g17702.t1 | isoform | g17702.t1 | 4233 | 5288 |
| HiC_scaffold_86 | g17702 | g17702.t1 | exon | g17702.t1.exon1 | 4233 | 4394 |
| HiC_scaffold_86 | g17702 | g17702.t1 | cds | g17702.t1.CDS1 | 4233 | 4394 |
| HiC_scaffold_86 | g17702 | g17702.t1 | exon | g17702.t1.exon2 | 4532 | 4660 |
| HiC_scaffold_86 | g17702 | g17702.t1 | cds | g17702.t1.CDS2 | 4532 | 4660 |
| HiC_scaffold_86 | g17702 | g17702.t1 | exon | g17702.t1.exon3 | 4732 | 5065 |
| HiC_scaffold_86 | g17702 | g17702.t1 | cds | g17702.t1.CDS3 | 4732 | 5065 |
| HiC_scaffold_86 | g17702 | g17702.t1 | exon | g17702.t1.exon4 | 5260 | 5288 |
| HiC_scaffold_86 | g17702 | g17702.t1 | cds | g17702.t1.CDS4 | 5260 | 5288 |
| HiC_scaffold_86 | g17702 | g17702.t1 | TSS | g17702.t1 | NA | NA |
| HiC_scaffold_86 | g17702 | g17702.t1 | TTS | g17702.t1 | NA | NA |
Sequences
>g17702.t1 Gene=g17702 Length=654
ATGCGGAACTGCAGTTTTTCAGATGTGATATCACAACAAAGCAATGGCACATCTTCACCA
TCATCACCACAACCACCTTCATCACTAAATTCTTCCAAAAAGTCTTCAGAAAATGGCAGT
AATCATCAACGACAGCGAAGTGGAAAACTTTTATTAGAAAATCTCAATATTACATCGTCA
AATGGCAGCGAAAGACCAAAGCCACAAATTCTTGAACTTGTAATAAACAAGGACAAATAT
GGCTACGGTATGAAAGTGTCAGGTGAAAATCCAGTATTTGTAGATAGTGTCAAAGAAGGT
GGTGCAGCTTTTCGTGCTGGTTTACATGCTGCCGATATGATTTTGCGTGTTAATGGACAT
AATAGAAATGCGAGAAATTTTGCATTACCACTTGGTGGTTCCAACAGTCCTGTTATTATT
GGTGCAACCACACCTAACACACCGACACCTACTAGTCAGAGAAATAGTATTACAGCACCA
CTGCCTGTTGATCACAACAAGCGAATGGAAGTAGAATTTACAAAAATGCATACACTCTTT
ATGATGCTCGAGCAGGAGAAGAAAAATCTCGAAAAATTGCGTGAGAATGAGTCACAAAAT
GGAAATGAATTGTGCGTGCTGAAGCAAATATTCGAACACTTCAAGAGCAATTAA
>g17702.t1 Gene=g17702 Length=217
MRNCSFSDVISQQSNGTSSPSSPQPPSSLNSSKKSSENGSNHQRQRSGKLLLENLNITSS
NGSERPKPQILELVINKDKYGYGMKVSGENPVFVDSVKEGGAAFRAGLHAADMILRVNGH
NRNARNFALPLGGSNSPVIIGATTPNTPTPTSQRNSITAPLPVDHNKRMEVEFTKMHTLF
MMLEQEKKNLEKLRENESQNGNELCVLKQIFEHFKSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g17702.t1 | CDD | cd00992 | PDZ_signaling | 70 | 121 | 4.66588E-10 |
| 6 | g17702.t1 | Coils | Coil | Coil | 176 | 203 | - |
| 5 | g17702.t1 | Gene3D | G3DSA:2.30.42.10 | - | 56 | 128 | 1.2E-13 |
| 9 | g17702.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 51 | - |
| 2 | g17702.t1 | PANTHER | PTHR45872:SF2 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D | 67 | 196 | 1.1E-28 |
| 3 | g17702.t1 | PANTHER | PTHR45872 | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D | 67 | 196 | 1.1E-28 |
| 1 | g17702.t1 | Pfam | PF00595 | PDZ domain | 77 | 127 | 1.1E-7 |
| 10 | g17702.t1 | ProSiteProfiles | PS50106 | PDZ domain profile. | 72 | 119 | 11.983 |
| 8 | g17702.t1 | SMART | SM00228 | pdz_new | 80 | 146 | 5.6E-5 |
| 4 | g17702.t1 | SUPERFAMILY | SSF50156 | PDZ domain-like | 65 | 122 | 1.73E-13 |
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:0005515 | protein binding | 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. There were no conditions that were differentially expressed