General information for g12724.t4
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.t4 | TTS | g12724.t4 | 25466936 | 25466936 |
| chr_1 | g12724 | g12724.t4 | isoform | g12724.t4 | 25467038 | 25468035 |
| chr_1 | g12724 | g12724.t4 | exon | g12724.t4.exon1 | 25467038 | 25467341 |
| chr_1 | g12724 | g12724.t4 | cds | g12724.t4.CDS1 | 25467039 | 25467341 |
| chr_1 | g12724 | g12724.t4 | exon | g12724.t4.exon2 | 25467405 | 25467554 |
| chr_1 | g12724 | g12724.t4 | cds | g12724.t4.CDS2 | 25467405 | 25467554 |
| chr_1 | g12724 | g12724.t4 | exon | g12724.t4.exon3 | 25467610 | 25467956 |
| chr_1 | g12724 | g12724.t4 | cds | g12724.t4.CDS3 | 25467610 | 25467956 |
| chr_1 | g12724 | g12724.t4 | exon | g12724.t4.exon4 | 25468026 | 25468035 |
| chr_1 | g12724 | g12724.t4 | cds | g12724.t4.CDS4 | 25468026 | 25468035 |
| chr_1 | g12724 | g12724.t4 | TSS | g12724.t4 | 25468311 | 25468311 |
Sequences
>g12724.t4 Gene=g12724 Length=811
ATGGAACAAGAAAATTCACAGAAAAAGACTCAAGAAGAGGAATTCAATTCCCAGCGTGCA
AAAATGAAAGAGATTTATTTAGCAAAAGAGAAGGAATGTGTACAGTTGAAACAAAAAATT
ATAAGTTTAAAGAAAGACCTTGATGAGGCTTCATCACAAATAGTCATTGCTGAGTACAAC
CGAGAAAAAGATTTAGAACGTTTTGAACAAGAGACATTGACTCTTAATCAAATAATTCAA
GAAACTTGTGACGAATCGACTATAGCTCAAACCGAAATAAAACGACTTCAAGAGGAAAAT
GAGAAAATTAAACAAGAAATGGCGCTATTAAGAGAAACATTGATACAACAGCAACAAGAA
TCAAATAAGAGTTTAGAATCTATTCTTGGACTAAAAACTTTAGCTAGAAATGTTAAGAAA
ATAACTGGAACACATAGTAATAGTCAAGAGAATTTAGATGAATCAATGCGAAAAGTAGCA
GCGACATCAGCTAGTGCAGCGAAATATGCTCAAGAAGATGCTGATACGTTAAGGTCATTA
GTTGTTCCTCTGGAAAGTGAAATTATACAATTAAAAGAAAAATTAAGAGCTGCATATGAC
GAAATTGAACTATTGAAAACTGCCAAAGGTGAAAGTATTCAAGTAAAATCAGCATTAGTT
GGTTTACTAGGTGAGACTCAAAAAGAAAATGAAGGTGATGTCAAAGAAGAACCAATGGAG
CAGGAAGAAACAGCAAAATCTCAAGAGTCATGTAATATGTGCAAAAATTATGAACTCCAG
TTAGTTCAAGCTCAAGAATCCATCGAGAATG
>g12724.t4 Gene=g12724 Length=270
MEQENSQKKTQEEEFNSQRAKMKEIYLAKEKECVQLKQKIISLKKDLDEASSQIVIAEYN
REKDLERFEQETLTLNQIIQETCDESTIAQTEIKRLQEENEKIKQEMALLRETLIQQQQE
SNKSLESILGLKTLARNVKKITGTHSNSQENLDESMRKVAATSASAAKYAQEDADTLRSL
VVPLESEIIQLKEKLRAAYDEIELLKTAKGESIQVKSALVGLLGETQKENEGDVKEEPME
QEETAKSQESCNMCKNYELQLVQAQESIEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12724.t4 | Coils | Coil | Coil | 1 | 21 | - |
| 9 | g12724.t4 | Coils | Coil | Coil | 26 | 53 | - |
| 8 | g12724.t4 | Coils | Coil | Coil | 79 | 120 | - |
| 6 | g12724.t4 | Coils | Coil | Coil | 188 | 208 | - |
| 4 | g12724.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 247 | - |
| 5 | g12724.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 244 | - |
| 2 | g12724.t4 | PANTHER | PTHR31179:SF7 | RABAPTIN (RAB EFFECTOR) | 5 | 207 | 9.5E-22 |
| 3 | g12724.t4 | PANTHER | PTHR31179 | RAB GTPASE-BINDING EFFECTOR PROTEIN | 5 | 207 | 9.5E-22 |
| 1 | g12724.t4 | Pfam | PF03528 | Rabaptin | 8 | 209 | 3.5E-9 |
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:0008083 | growth factor activity | 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.
