General information for g13727.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cytoplasmic dynein 1 light intermediate chain 1.
Parent gene
- The parent gene g13727 is located on chr_1: 32085225..32095357 (+ 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 | g13727 | g13727.t4 | TSS | g13727.t4 | 32084330 | 32084330 |
| chr_1 | g13727 | g13727.t4 | isoform | g13727.t4 | 32085225 | 32085914 |
| chr_1 | g13727 | g13727.t4 | exon | g13727.t4.exon1 | 32085225 | 32085849 |
| chr_1 | g13727 | g13727.t4 | cds | g13727.t4.CDS1 | 32085332 | 32085849 |
| chr_1 | g13727 | g13727.t4 | exon | g13727.t4.exon2 | 32085908 | 32085914 |
| chr_1 | g13727 | g13727.t4 | cds | g13727.t4.CDS2 | 32085908 | 32085914 |
| chr_1 | g13727 | g13727.t4 | TTS | g13727.t4 | 32086642 | 32086642 |
Sequences
>g13727.t4 Gene=g13727 Length=632
GACTTGGTGTGTGGATTTTAGACGGTGATATTGGACATCTGAATCTCTTAAAATTTGCAC
TTAACGAGAAAAATTACGCTCACACACTGGTTATACTTGCAATTTCAATGACGACACCTT
GGAATTGGCAAGAACAACTCGAACATTGGATGAAAGTTCTTGGGGATCATTTAGAACAAT
TAAAAATATCATCTGAAGAACGTCAAGCTGAGAAGCAGCGATTAGTAAATTTGTGGCAAA
CTTATTGTGAAACTGCCGATGAACTTGATCCCAGCTCACCGATGAAACGAAATAATAGAC
TTTCATCAGTAGACGACGACTTAGATCTAATGCCATTACCTGATGGTTGTTTAGTAACAA
ATCATGGACTCGACATTGTAGTTGTCATCACAAAAACAGATTATATGATCACACTCGAAA
AAGAGTTTGATTATAGAGAAGAGCACTTTGACTTTATGCAGCAATGGATTCGAAGATTTT
GTCTTCATTATGGAGCATCATTATTTTATACCAGTGTTAAAGAAGATAAAAACTGTGATT
TATTATATAAATATTTAACACATCGAATCTACGATTTGCCATTTAGAACACCAGCATTAG
TTGTGGAAAAAGATGCAGTATTAATACCAGCG
>g13727.t4 Gene=g13727 Length=175
MTTPWNWQEQLEHWMKVLGDHLEQLKISSEERQAEKQRLVNLWQTYCETADELDPSSPMK
RNNRLSSVDDDLDLMPLPDGCLVTNHGLDIVVVITKTDYMITLEKEFDYREEHFDFMQQW
IRRFCLHYGASLFYTSVKEDKNCDLLYKYLTHRIYDLPFRTPALVVEKDAVLIPA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13727.t4 | PANTHER | PTHR12688 | DYNEIN LIGHT INTERMEDIATE CHAIN | 1 | 175 | 0.00e+00 |
| 1 | g13727.t4 | Pfam | PF05783 | Dynein light intermediate chain (DLIC) | 1 | 175 | 0.00e+00 |
| 3 | g13727.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 86 | 157 | 3.22e-05 |
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.
