General information for g13860.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t10 | TSS | g13860.t10 | 32879368 | 32879368 |
| chr_1 | g13860 | g13860.t10 | isoform | g13860.t10 | 32879842 | 32884761 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon1 | 32879842 | 32879984 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon2 | 32880042 | 32880185 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon3 | 32880245 | 32880379 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon4 | 32883438 | 32883638 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon5 | 32883699 | 32883855 |
| chr_1 | g13860 | g13860.t10 | cds | g13860.t10.CDS1 | 32883728 | 32883855 |
| chr_1 | g13860 | g13860.t10 | exon | g13860.t10.exon6 | 32883927 | 32884761 |
| chr_1 | g13860 | g13860.t10 | cds | g13860.t10.CDS2 | 32883927 | 32884761 |
| chr_1 | g13860 | g13860.t10 | TTS | g13860.t10 | 32885311 | 32885311 |
Sequences
>g13860.t10 Gene=g13860 Length=1615
ATGGATAGAAAGGCCGAGCTTGAACGCAAAAAGGCAAAATTACAAGCCTTGCGTGATGAA
AAGGAAAAGAGGAGACGTGAGAAAGAAGAAAAGGACCTGCAGGAAGCTAAGGCTGGAGCT
CCTTCAGAAAAAGACACAAGAAAGGATTTAGATGAAATGTTGTCTTCTTTAGGTGTTGCC
CCAGTTTCTGAAGTTCTTTCATCACTTTCTTCTGTTACCTCTGTTACATCCGATCAGTCT
GGTCAAACGCCAGATGCTAGCCTTCAACCAACACTAAATGGACAAAATACGAAAGCAAAA
AAACAACAAACGCTATCAGTTGTACAAGTGCAGGTCACTAATATTCAACCAAAGGAGAAT
GTTACATATACAAAGCAGACACAAACGACAAGTTCAGGCACTCATGAGTTACGAGATGGT
GACAATGTTGAGTTTTACTTATACAGTGCTTACTTTTGGGGACGCACAAGGCGATGACGA
GGACCATTCGTTATCTCATTTGGATCATGGTGGATTTCATTCAAAATTACCTCCTGGAAT
TCTCCCTCATGGTTTACCGACAGTCAAAGAAGTCGCTCCAGCAATTACACCACAAGAACA
GAAGAAAGATGATATTAAACAAGTAAAAGAACTTTCAGAAGAACAAAAGCAAATGATTAT
CTTATCAGAGGATTTTCAACGTTTTGTTTTACGCTCTGGAAGAGTTATGGAACGCGCACT
GTCAGAAACTGTTGATATTTATACAGATTATATAGGAGGTAGTGAATCTGATGAAGGACT
AGATGAAAAGTCTCATGCTCGGTTATCATTGAATCGAATATTTTACGATGACAGATGGTC
AAAGAATCGTTGTGTTACATCATTTGATTGGTCAACCCATTTTCCTGAACTCATGGTCGC
TTCTTATCACAATAACGAAGAATTACCAAATGAACCAGATGGCGTTGTTGTTGTTTGGAA
TACAAAATTTAAGAAACAAACACCTGAAGATGTTTTTCATTGTCAAAGTGCAGTCATGTC
AACATGTTTCGCTAAATTTCATCCTAATTTGATACTAGGTGGTACTTATTCAGGACAGAT
AGTACTGTGGGATAATCGTGTTCAAAAGCGTACGCCAATACAACGAACACCACTTAGTTC
GACTGCCCATACTCATCCAGTCTATTGCTTGTCAATGGTGGGAACACAAAATGCTCATAA
TGTTATTTCAATTTCGTCAGACGGTCGTTTATGTTCATGGAGTTTAGACATGTTATCAGC
TCCTCAAGATACTCTCGAATTACAACAAAAACAGCCAAAACCAATCGCAGTCACATGCAT
GTCATTCCTTCATGATGAAGTCAATAATTTTGTATTAGGTAGTGAAGATGGATATGTGCA
TTCAGCATCGCGTCATGGTAATCGTTCGGGTATTATTGAAACTTATGAAAAACATTTAGG
ACCTGTAACAGGAATTTCAACTCATCAAAGTCATACTACTGCAGAGTTTTCACATTTATT
CCTTACATCTTCAATTGATTGGACAATTAAATTGTGGAGTTTGAAAGACACAAAGCCACT
TTATTCATTTGAAGACAATTCTGATTATGTGATGGATGTTGCTTGGTCGCCAATT
>g13860.t10 Gene=g13860 Length=321
MIILSEDFQRFVLRSGRVMERALSETVDIYTDYIGGSESDEGLDEKSHARLSLNRIFYDD
RWSKNRCVTSFDWSTHFPELMVASYHNNEELPNEPDGVVVVWNTKFKKQTPEDVFHCQSA
VMSTCFAKFHPNLILGGTYSGQIVLWDNRVQKRTPIQRTPLSSTAHTHPVYCLSMVGTQN
AHNVISISSDGRLCSWSLDMLSAPQDTLELQQKQPKPIAVTCMSFLHDEVNNFVLGSEDG
YVHSASRHGNRSGIIETYEKHLGPVTGISTHQSHTTAEFSHLFLTSSIDWTIKLWSLKDT
KPLYSFEDNSDYVMDVAWSPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13860.t10 | Gene3D | G3DSA:2.130.10.10 | - | 58 | 203 | 0.000 |
| 10 | g13860.t10 | Gene3D | G3DSA:2.130.10.10 | - | 204 | 321 | 0.000 |
| 2 | g13860.t10 | PANTHER | PTHR12442:SF22 | CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN-RELATED | 1 | 321 | 0.000 |
| 3 | g13860.t10 | PANTHER | PTHR12442 | DYNEIN INTERMEDIATE CHAIN | 1 | 321 | 0.000 |
| 1 | g13860.t10 | Pfam | PF00400 | WD domain, G-beta repeat | 257 | 296 | 0.210 |
| 11 | g13860.t10 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 96 | 321 | 10.891 |
| 8 | g13860.t10 | SMART | SM00320 | WD40_4 | 108 | 147 | 2.000 |
| 6 | g13860.t10 | SMART | SM00320 | WD40_4 | 157 | 197 | 4.100 |
| 7 | g13860.t10 | SMART | SM00320 | WD40_4 | 207 | 246 | 260.000 |
| 5 | g13860.t10 | SMART | SM00320 | WD40_4 | 251 | 296 | 0.012 |
| 4 | g13860.t10 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 65 | 320 | 0.000 |
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:0005515 | protein binding | 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.
