General information for g17217.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17217 is located on chr_4: 12850854..12854621 (- 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_4 | g17217 | g17217.t23 | TTS | g17217.t23 | 12850741 | 12850741 |
| chr_4 | g17217 | g17217.t23 | isoform | g17217.t23 | 12850854 | 12854621 |
| chr_4 | g17217 | g17217.t23 | exon | g17217.t23.exon1 | 12850854 | 12851526 |
| chr_4 | g17217 | g17217.t23 | cds | g17217.t23.CDS1 | 12850854 | 12851375 |
| chr_4 | g17217 | g17217.t23 | exon | g17217.t23.exon2 | 12854616 | 12854621 |
| chr_4 | g17217 | g17217.t23 | TSS | g17217.t23 | NA | NA |
Sequences
>g17217.t23 Gene=g17217 Length=679
TCTTAGAGAAAATAATAATGATGTTAAAACAACTGTTGATGAAGATATTGTTACGGAAGA
GCAAAATGACTCAGGCATTGGCACTGATGCATCTTCAGTGTCTTCTGACGCGAGCTACCA
AACTGTTTTGAGCAACACTTCTATTTCTTTAGATTCGATGAATATAAATAGCTCAGAAGA
AGATGAAAAGAATGCTGATGCACAACTGGATTTTGCTCTAGAAGACACTCTTGAATTAAT
AATTGAACGAGATGATAAAGAAATTCCATTAAACATGGACAAAACTGCGACAATTTCTGA
TGTTCTTAATCAAGCATCTTTAATTGGAAATTTTACAAGTGATGATTTTGATTTGTCAAT
TGATAGCAAAACTTTACCACGAACAATCAGTCTTCGTGATGCAGCCATCACTTATGGAAG
TCGCATTCGTTTAGTTGAGCGTCCATTTCAAATTTTTATTCGTCGTGTTGATGGTCGCAT
TTTGACTTTGGATGTCACTTCCTCAAACACTATTGAATATTTGAAAGAACGATTCAATTA
CACTGATCAAGTTCCAATTCATCAACAAAGATTGTTGTATCAAAGTCAAGAATTGGAAAA
TTCACGTACTTTGCAATTTTATAAAATTCGCAAAAATGCAACACTTGAAATGGTCTACAG
ACTTCGTGGTGGATTTTAA
>g17217.t23 Gene=g17217 Length=173
MNINSSEEDEKNADAQLDFALEDTLELIIERDDKEIPLNMDKTATISDVLNQASLIGNFT
SDDFDLSIDSKTLPRTISLRDAAITYGSRIRLVERPFQIFIRRVDGRILTLDVTSSNTIE
YLKERFNYTDQVPIHQQRLLYQSQELENSRTLQFYKIRKNATLEMVYRLRGGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g17217.t23 | Gene3D | G3DSA:3.10.20.90 | - | 94 | 173 | 0.0000000 |
| 3 | g17217.t23 | PANTHER | PTHR10666 | UBIQUITIN | 32 | 141 | 0.0000000 |
| 5 | g17217.t23 | PANTHER | PTHR10666:SF336 | POLYUBIQUITIN-LIKE | 32 | 141 | 0.0000000 |
| 2 | g17217.t23 | PANTHER | PTHR10666 | UBIQUITIN | 97 | 172 | 0.0000000 |
| 4 | g17217.t23 | PANTHER | PTHR10666:SF336 | POLYUBIQUITIN-LIKE | 97 | 172 | 0.0000000 |
| 6 | g17217.t23 | PRINTS | PR00348 | Ubiquitin signature | 107 | 127 | 0.0000000 |
| 7 | g17217.t23 | PRINTS | PR00348 | Ubiquitin signature | 128 | 148 | 0.0000000 |
| 8 | g17217.t23 | PRINTS | PR00348 | Ubiquitin signature | 149 | 170 | 0.0000000 |
| 1 | g17217.t23 | Pfam | PF00240 | Ubiquitin family | 99 | 170 | 0.0000000 |
| 14 | g17217.t23 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 97 | 172 | 19.7820000 |
| 11 | g17217.t23 | SMART | SM00213 | ubq_7 | 25 | 95 | 18.0000000 |
| 12 | g17217.t23 | SMART | SM00213 | ubq_7 | 97 | 168 | 0.0000000 |
| 9 | g17217.t23 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 32 | 95 | 0.0000052 |
| 10 | g17217.t23 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 95 | 172 | 0.0000000 |
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