General information for g13860.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytoplasmic dynein 1 intermediate chain.
Parent gene
- The parent gene g13860 is located on chr_1: 32880395..32885112 (+ 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 | g13860 | g13860.t2 | isoform | g13860.t2 | 32879315 | 32881308 |
| chr_1 | g13860 | g13860.t2 | exon | g13860.t2.exon1 | 32879315 | 32879393 |
| chr_1 | g13860 | g13860.t2 | TSS | g13860.t2 | 32879368 | 32879368 |
| chr_1 | g13860 | g13860.t2 | exon | g13860.t2.exon2 | 32879750 | 32879984 |
| chr_1 | g13860 | g13860.t2 | cds | g13860.t2.CDS1 | 32879842 | 32879984 |
| chr_1 | g13860 | g13860.t2 | exon | g13860.t2.exon3 | 32880042 | 32880185 |
| chr_1 | g13860 | g13860.t2 | cds | g13860.t2.CDS2 | 32880042 | 32880185 |
| chr_1 | g13860 | g13860.t2 | exon | g13860.t2.exon4 | 32880245 | 32880375 |
| chr_1 | g13860 | g13860.t2 | cds | g13860.t2.CDS3 | 32880245 | 32880375 |
| chr_1 | g13860 | g13860.t2 | exon | g13860.t2.exon5 | 32881288 | 32881308 |
| chr_1 | g13860 | g13860.t2 | cds | g13860.t2.CDS4 | 32881288 | 32881307 |
| chr_1 | g13860 | g13860.t2 | TTS | g13860.t2 | NA | NA |
Sequences
>g13860.t2 Gene=g13860 Length=610
TTCTATAATAAGTTTAACAGTCGTATGAAATTTAAATGACTGCATGCTGTCAGAAAAAAA
TTAGTTGAGAAAAGATTGGTATTACATTTCGTTTTCACTTTGTTCGATGATGTCGGCAAC
ATTAGATCAGCAAAACTGGATAGTCTAGATCGTCTCAAACAATTATCTAAAATGGATAGA
AAGGCCGAGCTTGAACGCAAAAAGGCAAAATTACAAGCCTTGCGTGATGAAAAGGAAAAG
AGGAGACGTGAGAAAGAAGAAAAGGACCTGCAGGAAGCTAAGGCTGGAGCTCCTTCAGAA
AAAGACACAAGAAAGGATTTAGATGAAATGTTGTCTTCTTTAGGTGTTGCCCCAGTTTCT
GAAGTTCTTTCATCACTTTCTTCTGTTACCTCTGTTACATCCGATCAGTCTGGTCAAACG
CCAGATGCTAGCCTTCAACCAACACTAAATGGACAAAATACGAAAGCAAAAAAACAACAA
ACGCTATCAGTTGTACAAGTGCAGGTCACTAATATTCAACCAAAGGAGAATGTTACATAT
ACAAAGCAGACACAAACGACAAGTTCAGGCACTCATGAGTTACGAGATGCACATGCAACC
GATTATTATG
>g13860.t2 Gene=g13860 Length=146
MDRKAELERKKAKLQALRDEKEKRRREKEEKDLQEAKAGAPSEKDTRKDLDEMLSSLGVA
PVSEVLSSLSSVTSVTSDQSGQTPDASLQPTLNGQNTKAKKQQTLSVVQVQVTNIQPKEN
VTYTKQTQTTSSGTHELRDAHATDYY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13860.t2 | Coils | Coil | Coil | 4 | 37 | - |
| 2 | g13860.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 52 | - |
| 3 | g13860.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 66 | 102 | - |
| 4 | g13860.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 123 | 146 | - |
| 1 | g13860.t2 | Pfam | PF11540 | Cytoplasmic dynein 1 intermediate chain 2 | 100 | 130 | 9.3E-12 |
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:0007018 | microtubule-based movement | BP |
| GO:0005868 | cytoplasmic dynein complex | CC |
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.
