General information for g13860.t3
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.t3 | isoform | g13860.t3 | 32879315 | 32885112 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon1 | 32879315 | 32879442 |
| chr_1 | g13860 | g13860.t3 | TSS | g13860.t3 | 32879368 | 32879368 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon2 | 32879796 | 32879984 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS1 | 32879842 | 32879984 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon3 | 32880042 | 32880185 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS2 | 32880042 | 32880185 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon4 | 32880245 | 32880375 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS3 | 32880245 | 32880375 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon5 | 32881288 | 32881308 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS4 | 32881288 | 32881308 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon6 | 32883462 | 32883638 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS5 | 32883462 | 32883638 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon7 | 32883699 | 32883855 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS6 | 32883699 | 32883855 |
| chr_1 | g13860 | g13860.t3 | exon | g13860.t3.exon8 | 32883927 | 32885112 |
| chr_1 | g13860 | g13860.t3 | cds | g13860.t3.CDS7 | 32883927 | 32885112 |
| chr_1 | g13860 | g13860.t3 | TTS | g13860.t3 | 32885311 | 32885311 |
Sequences
>g13860.t3 Gene=g13860 Length=2133
TTCTATAATAAGTTTAACAGTCGTATGAAATTTAAATGACTGCATGCTGTCAGAAAAAAA
TTAGTTGAGAAAAGATTGGAATAACATTTTTCTTAAAATAAAATAAAGAAATTTCGCTGA
TCAAATTGATCAGCAAAACTGGATAGTCTAGATCGTCTCAAACAATTATCTAAAATGGAT
AGAAAGGCCGAGCTTGAACGCAAAAAGGCAAAATTACAAGCCTTGCGTGATGAAAAGGAA
AAGAGGAGACGTGAGAAAGAAGAAAAGGACCTGCAGGAAGCTAAGGCTGGAGCTCCTTCA
GAAAAAGACACAAGAAAGGATTTAGATGAAATGTTGTCTTCTTTAGGTGTTGCCCCAGTT
TCTGAAGTTCTTTCATCACTTTCTTCTGTTACCTCTGTTACATCCGATCAGTCTGGTCAA
ACGCCAGATGCTAGCCTTCAACCAACACTAAATGGACAAAATACGAAAGCAAAAAAACAA
CAAACGCTATCAGTTGTACAAGTGCAGGTCACTAATATTCAACCAAAGGAGAATGTTACA
TATACAAAGCAGACACAAACGACAAGTTCAGGCACTCATGAGTTACGAGATGCACATGCA
ACCGATTATTATGTGCTTACTTTTGGGGACGCACAAGGCGATGACGAGGACCATTCGTTA
TCTCATTTGGATCATGGTGGATTTCATTCAAAATTACCTCCTGGAATTCTCCCTCATGGT
TTACCGACAGTCAAAGAAGTCGCTCCAGCAATTACACCACAAGAACAGAAGAAAGATGAT
ATTAAACAAGTAAAAGAACTTTCAGAAGAACAAAAGCAAATGATTATCTTATCAGAGGAT
TTTCAACGTTTTGTTTTACGCTCTGGAAGAGTTATGGAACGCGCACTGTCAGAAACTGTT
GATATTTATACAGATTATATAGGAGGTAGTGAATCTGATGAAGGACTAGATGAAAAGTCT
CATGCTCGGTTATCATTGAATCGAATATTTTACGATGACAGATGGTCAAAGAATCGTTGT
GTTACATCATTTGATTGGTCAACCCATTTTCCTGAACTCATGGTCGCTTCTTATCACAAT
AACGAAGAATTACCAAATGAACCAGATGGCGTTGTTGTTGTTTGGAATACAAAATTTAAG
AAACAAACACCTGAAGATGTTTTTCATTGTCAAAGTGCAGTCATGTCAACATGTTTCGCT
AAATTTCATCCTAATTTGATACTAGGTGGTACTTATTCAGGACAGATAGTACTGTGGGAT
AATCGTGTTCAAAAGCGTACGCCAATACAACGAACACCACTTAGTTCGACTGCCCATACT
CATCCAGTCTATTGCTTGTCAATGGTGGGAACACAAAATGCTCATAATGTTATTTCAATT
TCGTCAGACGGTCGTTTATGTTCATGGAGTTTAGACATGTTATCAGCTCCTCAAGATACT
CTCGAATTACAACAAAAACAGCCAAAACCAATCGCAGTCACATGCATGTCATTCCTTCAT
GATGAAGTCAATAATTTTGTATTAGGTAGTGAAGATGGATATGTGCATTCAGCATCGCGT
CATGGTAATCGTTCGGGTATTATTGAAACTTATGAAAAACATTTAGGACCTGTAACAGGA
ATTTCAACTCATCAAAGTCATACTACTGCAGAGTTTTCACATTTATTCCTTACATCTTCA
ATTGATTGGACAATTAAATTGTGGAGTTTGAAAGACACAAAGCCACTTTATTCATTTGAA
GACAATTCTGATTATGTGATGGATGTTGCTTGGTCGCCAATTCATCCATCTCTTTTTGCG
GCTGTTGATGGAAGTGGACGATTAGATTTGTGGAATTTGAATCAAGACACGGAAGTGCCA
ACATGCTCAGTTGTTGTAGAAGGAGCTCCAGCATTAAATCGTGTTTCATGGACACCTTCA
GGTTTGCATGTAACAATTGGTGATGAATCGGGCAAAATTTATGTTTATGATGTAGCTGAT
AATGTAGCTCAGCCAAGAATGGATGAATGGCAACGGTTTGGAACAACATTACATGAATTA
AAAATGAACACAAATGAAGACTTTGAAGATTTAGACAAATCAATGTCCATTCCACAACAA
CCTTTATCGCTGACAGGATCTTCTGTTGCGTAA
>g13860.t3 Gene=g13860 Length=652
MDRKAELERKKAKLQALRDEKEKRRREKEEKDLQEAKAGAPSEKDTRKDLDEMLSSLGVA
PVSEVLSSLSSVTSVTSDQSGQTPDASLQPTLNGQNTKAKKQQTLSVVQVQVTNIQPKEN
VTYTKQTQTTSSGTHELRDAHATDYYVLTFGDAQGDDEDHSLSHLDHGGFHSKLPPGILP
HGLPTVKEVAPAITPQEQKKDDIKQVKELSEEQKQMIILSEDFQRFVLRSGRVMERALSE
TVDIYTDYIGGSESDEGLDEKSHARLSLNRIFYDDRWSKNRCVTSFDWSTHFPELMVASY
HNNEELPNEPDGVVVVWNTKFKKQTPEDVFHCQSAVMSTCFAKFHPNLILGGTYSGQIVL
WDNRVQKRTPIQRTPLSSTAHTHPVYCLSMVGTQNAHNVISISSDGRLCSWSLDMLSAPQ
DTLELQQKQPKPIAVTCMSFLHDEVNNFVLGSEDGYVHSASRHGNRSGIIETYEKHLGPV
TGISTHQSHTTAEFSHLFLTSSIDWTIKLWSLKDTKPLYSFEDNSDYVMDVAWSPIHPSL
FAAVDGSGRLDLWNLNQDTEVPTCSVVVEGAPALNRVSWTPSGLHVTIGDESGKIYVYDV
ADNVAQPRMDEWQRFGTTLHELKMNTNEDFEDLDKSMSIPQQPLSLTGSSVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13860.t3 | Coils | Coil | Coil | 4 | 37 | - |
| 6 | g13860.t3 | Gene3D | G3DSA:2.130.10.10 | - | 275 | 419 | 1.7E-14 |
| 5 | g13860.t3 | Gene3D | G3DSA:2.130.10.10 | - | 420 | 627 | 1.6E-28 |
| 15 | g13860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 52 | - |
| 14 | g13860.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 66 | 101 | - |
| 2 | g13860.t3 | PANTHER | PTHR12442:SF22 | CYTOPLASMIC DYNEIN 1 INTERMEDIATE CHAIN-RELATED | 3 | 625 | 8.8E-218 |
| 3 | g13860.t3 | PANTHER | PTHR12442 | DYNEIN INTERMEDIATE CHAIN | 3 | 625 | 8.8E-218 |
| 1 | g13860.t3 | Pfam | PF11540 | Cytoplasmic dynein 1 intermediate chain 2 | 100 | 130 | 7.3E-11 |
| 16 | g13860.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 311 | 608 | 15.188 |
| 10 | g13860.t3 | SMART | SM00320 | WD40_4 | 323 | 362 | 2.0 |
| 8 | g13860.t3 | SMART | SM00320 | WD40_4 | 372 | 412 | 4.1 |
| 12 | g13860.t3 | SMART | SM00320 | WD40_4 | 422 | 461 | 260.0 |
| 13 | g13860.t3 | SMART | SM00320 | WD40_4 | 466 | 511 | 0.012 |
| 11 | g13860.t3 | SMART | SM00320 | WD40_4 | 514 | 554 | 0.0029 |
| 9 | g13860.t3 | SMART | SM00320 | WD40_4 | 561 | 599 | 13.0 |
| 4 | g13860.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 278 | 603 | 3.85E-40 |
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:0005515 | protein binding | MF |
| GO:0005868 | cytoplasmic dynein complex | CC |
KEGG
Orthology
- This transcript has been annotated with K10415 (dynein cytoplasmic 1 intermediate chain)
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.
