General information for g12724.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12724 is located on chr_1: 25467038..25468035 (- 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_1 | g12724 | g12724.t2 | TTS | g12724.t2 | 25465791 | 25465791 |
| chr_1 | g12724 | g12724.t2 | isoform | g12724.t2 | 25465894 | 25467038 |
| chr_1 | g12724 | g12724.t2 | exon | g12724.t2.exon1 | 25465894 | 25466084 |
| chr_1 | g12724 | g12724.t2 | cds | g12724.t2.CDS1 | 25465894 | 25466084 |
| chr_1 | g12724 | g12724.t2 | exon | g12724.t2.exon2 | 25466141 | 25467038 |
| chr_1 | g12724 | g12724.t2 | cds | g12724.t2.CDS2 | 25466141 | 25467032 |
| chr_1 | g12724 | g12724.t2 | TSS | g12724.t2 | NA | NA |
Sequences
>g12724.t2 Gene=g12724 Length=1089
GAAAAGATGAAAATAGTAAAAGTAGAAAAAATAGTTGATCGTTTAAAGCAAGATTTACTG
AAAGAGTCGGCACTTCGACTCGATTTAGAGAAGACGTGGCAAGAAAAACGTGAAGAGCAT
CGAGATGCTGTTCAAAAATTATGTGACAAATTAAATGAAAGTGAAAGGCAGATGATTCAG
CTACAAACTGAATTTGGCAATTTCAAAGATGAAATAAGTAATGAGTTAAAAAAGAATTTT
GGTGAACGGCAAGACATCTTTGATCATTTAGAAACTCTTCAAAATGATAATGAATACTTA
AGTGGACGATATTTAGAACATTCAAATGAAATGAAAGATAAAGAAATAAATCTGCCACAA
AGTATAGAAGAGCTACACGAATTTATTTTAGATCTTAATGAAAAGTTGATTGTATCAAAA
GTTGGGCAAGAATTTAATGAAGCAAAATGTGTTACATTTAGAGATGAGTCAAATATATTA
CGCGAACAATTACATCAAAAAGAAAAGGAAAAACAGTTTCTTGAGCAAAAATTAAACCAT
AGAATTCACAGTCTTGAGGATAAATTGAAACAAAATCATCAAAGTCATTTGAAGCTCATT
AGCGAGAAAGAGGAACTGCTGAAAGTGGAAAATGATAATAAAAAAGAAATTAGTGATTTG
CGAATGCAAAATATTGAACTGAGTGAGAATGTAGATAGACTGGAGAAAGCAAATATTGAT
ATTAAATCTAAACTTTCCATGCTTCAACAAGAATTGTCCACAAGTGAACAAGTTCAAAAA
GATTTTGTCAAGTTATCACAATCATTACAAATGCAATTAGAGAAAATTCGTTCTGCTGAC
TCTCAAGTTCGTTGGCAAGATTTCGATGATGTTGATAATTGTCCAAATTGCAAGCAAGAA
TTCACTGTGACAAGAAGAAAAAGAAATTGCCGTCATTGTGGAACAATATTTTGTGAAAAA
TGTTGTGATCGTTCTGTCAAGAGTGGACCTTCCCAGAAAATAGCAAAAGTATGCGATCTT
TGCAATACAATTCTGCAATCGCACTGTGCTCCATATTTTAGTGAAAATGCTCCTCAAAGT
CCAATTTAG
>g12724.t2 Gene=g12724 Length=360
MKIVKVEKIVDRLKQDLLKESALRLDLEKTWQEKREEHRDAVQKLCDKLNESERQMIQLQ
TEFGNFKDEISNELKKNFGERQDIFDHLETLQNDNEYLSGRYLEHSNEMKDKEINLPQSI
EELHEFILDLNEKLIVSKVGQEFNEAKCVTFRDESNILREQLHQKEKEKQFLEQKLNHRI
HSLEDKLKQNHQSHLKLISEKEELLKVENDNKKEISDLRMQNIELSENVDRLEKANIDIK
SKLSMLQQELSTSEQVQKDFVKLSQSLQMQLEKIRSADSQVRWQDFDDVDNCPNCKQEFT
VTRRKRNCRHCGTIFCEKCCDRSVKSGPSQKIAKVCDLCNTILQSHCAPYFSENAPQSPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g12724.t2 | Coils | Coil | Coil | 35 | 69 | - |
| 11 | g12724.t2 | Coils | Coil | Coil | 155 | 175 | - |
| 10 | g12724.t2 | Coils | Coil | Coil | 215 | 249 | - |
| 8 | g12724.t2 | Gene3D | G3DSA:1.20.5.730 | Single helix bin | 241 | 292 | 1.5E-19 |
| 9 | g12724.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 293 | 345 | 6.4E-14 |
| 3 | g12724.t2 | PANTHER | PTHR31179:SF7 | RABAPTIN (RAB EFFECTOR) | 5 | 353 | 9.2E-65 |
| 4 | g12724.t2 | PANTHER | PTHR31179 | RAB GTPASE-BINDING EFFECTOR PROTEIN | 5 | 353 | 9.2E-65 |
| 2 | g12724.t2 | Pfam | PF09311 | Rabaptin-like protein | 5 | 278 | 9.1E-33 |
| 1 | g12724.t2 | Pfam | PF01363 | FYVE zinc finger | 282 | 344 | 5.7E-14 |
| 13 | g12724.t2 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 286 | 344 | 11.673 |
| 7 | g12724.t2 | SMART | SM00064 | fyve_4 | 278 | 345 | 4.1E-19 |
| 5 | g12724.t2 | SUPERFAMILY | SSF103652 | G protein-binding domain | 242 | 290 | 1.41E-18 |
| 6 | g12724.t2 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 282 | 350 | 8.63E-16 |
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:0046872 | metal ion binding | MF |
| GO:0006897 | endocytosis | BP |
| GO:0005096 | GTPase activator activity | 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.
