General information for g13860.t11
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.t11 | TSS | g13860.t11 | 32879368 | 32879368 |
| chr_1 | g13860 | g13860.t11 | isoform | g13860.t11 | 32880395 | 32885112 |
| chr_1 | g13860 | g13860.t11 | exon | g13860.t11.exon1 | 32880395 | 32880894 |
| chr_1 | g13860 | g13860.t11 | exon | g13860.t11.exon2 | 32883397 | 32883586 |
| chr_1 | g13860 | g13860.t11 | exon | g13860.t11.exon3 | 32883744 | 32883855 |
| chr_1 | g13860 | g13860.t11 | cds | g13860.t11.CDS1 | 32883782 | 32883855 |
| chr_1 | g13860 | g13860.t11 | exon | g13860.t11.exon4 | 32883927 | 32884255 |
| chr_1 | g13860 | g13860.t11 | cds | g13860.t11.CDS2 | 32883927 | 32884255 |
| chr_1 | g13860 | g13860.t11 | exon | g13860.t11.exon5 | 32884406 | 32885112 |
| chr_1 | g13860 | g13860.t11 | cds | g13860.t11.CDS3 | 32884406 | 32885112 |
| chr_1 | g13860 | g13860.t11 | TTS | g13860.t11 | 32885311 | 32885311 |
Sequences
>g13860.t11 Gene=g13860 Length=1838
ATATTTTAAAACGAAATTTTATTTCGCTTTGAATATCTCTCTACTAACACTTTTCTAATC
AAAATGTAGTAGGCAAAAATATTAGATATTCATTAAAAATTAATTCATTTTTTCCACTAA
AATTAAACTCACATCACATGGAGTCGTAGTTAGTTATTTATTTTTTTGTGGTTTAGTTAG
GCAAAATTATCTATACTTTTATTCTTATATTTTTGTGTTTGAATGTAATTTTTTCATATT
TAGTGAGGTTTTTTCCATATTTGAAAAATAAATTAACAATCATGCTTATAGAAACTATTC
GATAAATTCTATCTCAAACTATCTAATTAAAGATATATGTGCAGCTAATATATCTTTTAA
TTTAATCGTTTTACTGATGAAAAAACACATTACCTTATCGAAAACTCACTAATATTGAAA
TAAAATAACAAAAACAGTTCTTTCTTGTCATTCTTCGCCCATGTCAGGATTGATAGAAGA
TTGGTGGCGGCCAAGAAAAGAAATATCGAAAGAGAAAAGAAAGTTGTTATTCGGTTCTTA
GCAATGTTGAGTTTTACTTATACAGTGCTTACTTTTGGGGACGCACAAGGCGATGACGAG
GACCATTCGTTATCTCATTTGGATCATGGTGGATTTCATTCAAAATTACCTCCTGGAATT
CTCCCTCATGGTTTACCGACAGTCAAAGAAAGGATTTTCAACGTTTTGTTTTACGCTCTG
GAAGAGTTATGGAACGCGCACTGTCAGAAACTGTTGATATTTATACAGATTATATAGGAG
GTAGTGAATCTGATGAAGGACTAGATGAAAAGTCTCATGCTCGGTTATCATTGAATCGAA
TATTTTACGATGACAGATGGTCAAAGAATCGTTGTGTTACATCATTTGATTGGTCAACCC
ATTTTCCTGAACTCATGGTCGCTTCTTATCACAATAACGAAGAATTACCAAATGAACCAG
ATGGCGTTGTTGTTGTTTGGAATACAAAATTTAAGAAACAAACACCTGAAGATGTTTTTC
ATTGTCAAAGTGCAGTCATGTCAACATGTTTCGCTAAATTTCATCCTAATTTGATACTAG
GTGGTACTTATTCAGGACAGATAGTACTGTGGGATAATCGTGTTCAAAAGCCTCCTCAAG
ATACTCTCGAATTACAACAAAAACAGCCAAAACCAATCGCAGTCACATGCATGTCATTCC
TTCATGATGAAGTCAATAATTTTGTATTAGGTAGTGAAGATGGATATGTGCATTCAGCAT
CGCGTCATGGTAATCGTTCGGGTATTATTGAAACTTATGAAAAACATTTAGGACCTGTAA
CAGGAATTTCAACTCATCAAAGTCATACTACTGCAGAGTTTTCACATTTATTCCTTACAT
CTTCAATTGATTGGACAATTAAATTGTGGAGTTTGAAAGACACAAAGCCACTTTATTCAT
TTGAAGACAATTCTGATTATGTGATGGATGTTGCTTGGTCGCCAATTCATCCATCTCTTT
TTGCGGCTGTTGATGGAAGTGGACGATTAGATTTGTGGAATTTGAATCAAGACACGGAAG
TGCCAACATGCTCAGTTGTTGTAGAAGGAGCTCCAGCATTAAATCGTGTTTCATGGACAC
CTTCAGGTTTGCATGTAACAATTGGTGATGAATCGGGCAAAATTTATGTTTATGATGTAG
CTGATAATGTAGCTCAGCCAAGAATGGATGAATGGCAACGGTTTGGAACAACATTACATG
AATTAAAAATGAACACAAATGAAGACTTTGAAGATTTAGACAAATCAATGTCCATTCCAC
AACAACCTTTATCGCTGACAGGATCTTCTGTTGCGTAA
>g13860.t11 Gene=g13860 Length=369
MERALSETVDIYTDYIGGSESDEGLDEKSHARLSLNRIFYDDRWSKNRCVTSFDWSTHFP
ELMVASYHNNEELPNEPDGVVVVWNTKFKKQTPEDVFHCQSAVMSTCFAKFHPNLILGGT
YSGQIVLWDNRVQKPPQDTLELQQKQPKPIAVTCMSFLHDEVNNFVLGSEDGYVHSASRH
GNRSGIIETYEKHLGPVTGISTHQSHTTAEFSHLFLTSSIDWTIKLWSLKDTKPLYSFED
NSDYVMDVAWSPIHPSLFAAVDGSGRLDLWNLNQDTEVPTCSVVVEGAPALNRVSWTPSG
LHVTIGDESGKIYVYDVADNVAQPRMDEWQRFGTTLHELKMNTNEDFEDLDKSMSIPQQP
LSLTGSSVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g13860.t11 | Gene3D | G3DSA:2.130.10.10 | - | 40 | 138 | 1.100e-06 |
| 13 | g13860.t11 | Gene3D | G3DSA:2.130.10.10 | - | 139 | 340 | 0.000e+00 |
| 3 | g13860.t11 | PANTHER | PTHR12442:SF37 | CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN 2 | 1 | 134 | 0.000e+00 |
| 5 | g13860.t11 | PANTHER | PTHR12442 | DYNEIN INTERMEDIATE CHAIN | 1 | 134 | 0.000e+00 |
| 2 | g13860.t11 | PANTHER | PTHR12442:SF37 | CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN 2 | 136 | 348 | 0.000e+00 |
| 4 | g13860.t11 | PANTHER | PTHR12442 | DYNEIN INTERMEDIATE CHAIN | 136 | 348 | 0.000e+00 |
| 1 | g13860.t11 | Pfam | PF00400 | WD domain, G-beta repeat | 189 | 228 | 2.600e-01 |
| 14 | g13860.t11 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 190 | 325 | 1.503e+01 |
| 10 | g13860.t11 | SMART | SM00320 | WD40_4 | 90 | 129 | 2.000e+00 |
| 8 | g13860.t11 | SMART | SM00320 | WD40_4 | 133 | 178 | 2.400e+02 |
| 7 | g13860.t11 | SMART | SM00320 | WD40_4 | 183 | 228 | 1.200e-02 |
| 9 | g13860.t11 | SMART | SM00320 | WD40_4 | 231 | 271 | 2.900e-03 |
| 11 | g13860.t11 | SMART | SM00320 | WD40_4 | 278 | 316 | 1.300e+01 |
| 6 | g13860.t11 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 47 | 321 | 0.000e+00 |
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.
