General information for g8970.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Dynactin subunit 5.
Parent gene
- The parent gene g8970 is located on chr_2: 34263618..34265158 (+ 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_2 | g8970 | g8970.t1 | TSS | g8970.t1 | 34263312 | 34263312 |
| chr_2 | g8970 | g8970.t1 | isoform | g8970.t1 | 34263387 | 34264874 |
| chr_2 | g8970 | g8970.t1 | exon | g8970.t1.exon1 | 34263387 | 34263449 |
| chr_2 | g8970 | g8970.t1 | cds | g8970.t1.CDS1 | 34263387 | 34263449 |
| chr_2 | g8970 | g8970.t1 | exon | g8970.t1.exon2 | 34263504 | 34263552 |
| chr_2 | g8970 | g8970.t1 | cds | g8970.t1.CDS2 | 34263504 | 34263552 |
| chr_2 | g8970 | g8970.t1 | exon | g8970.t1.exon3 | 34263618 | 34263853 |
| chr_2 | g8970 | g8970.t1 | cds | g8970.t1.CDS3 | 34263618 | 34263853 |
| chr_2 | g8970 | g8970.t1 | exon | g8970.t1.exon4 | 34264665 | 34264874 |
| chr_2 | g8970 | g8970.t1 | cds | g8970.t1.CDS4 | 34264665 | 34264874 |
| chr_2 | g8970 | g8970.t1 | TTS | g8970.t1 | 34265025 | 34265025 |
Sequences
>g8970.t1 Gene=g8970 Length=558
ATGGAAATTTGTGACATGTATTATAATAAAGATGAGTTTGTAGAAACTGCATCAGGAAAT
AAAGTAAATCGACAAACTGTATTGTGTGGAAGTCAAAATATTGTATTGCATGGTAAAGTA
ATAGTTGATAAGGGAGCAATAATTCGTGGAGATCTGGCAAATGTGAGAACTGGAAGGTAT
TGTGTGATTTCAAAAAATGCAGTAGTTAGACCACCATTTAAACAATTTAGCAAAGGAGTT
GCTTTCTTCCCTCTTCATATTGGAGATCATGTTTATATTGGTGAAAATTCTGTTGTGAGT
GCTGCAAGTATTGGATCTTATGTTTATATAGGCAAAAATGTTGTGATTGGACGAAGATGT
GTAATTAAAGATTGTACTATTATTGAAGATAACTCAGTATTGCCTCCTGAAACAACACTA
GCAAGTTTTATGAAATTTAATAATGATGGAACAATTGAGGGCGGACAGGGAACTGAATCG
GTTCCTGCGGCTATGCAAGACTTAATGGTTGATTTTACTAAATCATATTATGATCATTTT
TTAATGGCTAAATCTTAA
>g8970.t1 Gene=g8970 Length=185
MEICDMYYNKDEFVETASGNKVNRQTVLCGSQNIVLHGKVIVDKGAIIRGDLANVRTGRY
CVISKNAVVRPPFKQFSKGVAFFPLHIGDHVYIGENSVVSAASIGSYVYIGKNVVIGRRC
VIKDCTIIEDNSVLPPETTLASFMKFNNDGTIEGGQGTESVPAAMQDLMVDFTKSYYDHF
LMAKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8970.t1 | CDD | cd03359 | LbH_Dynactin_5 | 13 | 177 | 0.0e+00 |
| 5 | g8970.t1 | Gene3D | G3DSA:2.160.10.10 | Hexapeptide repeat proteins | 18 | 184 | 0.0e+00 |
| 3 | g8970.t1 | PANTHER | PTHR46126 | DYNACTIN SUBUNIT 5 | 1 | 182 | 0.0e+00 |
| 2 | g8970.t1 | Pfam | PF14602 | Hexapeptide repeat of succinyl-transferase | 84 | 101 | 8.0e-02 |
| 1 | g8970.t1 | Pfam | PF00132 | Bacterial transferase hexapeptide (six repeats) | 103 | 134 | 3.5e-06 |
| 4 | g8970.t1 | SUPERFAMILY | SSF51161 | Trimeric LpxA-like enzymes | 8 | 142 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K10427 (dynactin 5)
Pathway
- This transcript belongs to the following pathways
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.
