General information for g13727.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t2 | TSS | g13727.t2 | 32084330 | 32084330 |
| chr_1 | g13727 | g13727.t2 | isoform | g13727.t2 | 32084421 | 32086212 |
| chr_1 | g13727 | g13727.t2 | exon | g13727.t2.exon1 | 32084421 | 32084497 |
| chr_1 | g13727 | g13727.t2 | cds | g13727.t2.CDS1 | 32084421 | 32084497 |
| chr_1 | g13727 | g13727.t2 | exon | g13727.t2.exon2 | 32084967 | 32085157 |
| chr_1 | g13727 | g13727.t2 | cds | g13727.t2.CDS2 | 32084967 | 32085157 |
| chr_1 | g13727 | g13727.t2 | exon | g13727.t2.exon3 | 32085216 | 32085849 |
| chr_1 | g13727 | g13727.t2 | cds | g13727.t2.CDS3 | 32085216 | 32085849 |
| chr_1 | g13727 | g13727.t2 | exon | g13727.t2.exon4 | 32085908 | 32086212 |
| chr_1 | g13727 | g13727.t2 | cds | g13727.t2.CDS4 | 32085908 | 32086211 |
| chr_1 | g13727 | g13727.t2 | TTS | g13727.t2 | 32086642 | 32086642 |
Sequences
>g13727.t2 Gene=g13727 Length=1207
ATGGAGACTTCAACACAAATAAATGGACTCTCACCTGCAAAAAAGAAGGATAATGCAGAA
ACAAAGGAGAATTTATGGTCAGAAATTCTTGGTGAAGTTCAAAAACAAGGCACAGCTAAA
TTACCGTCAAATAAATGTGTGTTAGTACTAGGAGACAACTCATCTGGGAAAACGTCACTT
ATTGCAAAATTGCAAGGTGTAGAAGATCCTAAAAAAGGTTCTGGATTAGAATATGCATAC
ATTGATGTGAGGGATGAATATCGAGATGATCTAACACGACTTGGTGTGTGGATTTTAGAC
GGTGATATTGGACATCTGAATCTCTTAAAATTTGCACTTAACGAGAAAAATTACGCTCAC
ACACTGGTTATACTTGCAATTTCAATGACGACACCTTGGAATTGGCAAGAACAACTCGAA
CATTGGATGAAAGTTCTTGGGGATCATTTAGAACAATTAAAAATATCATCTGAAGAACGT
CAAGCTGAGAAGCAGCGATTAGTAAATTTGTGGCAAACTTATTGTGAAACTGCCGATGAA
CTTGATCCCAGCTCACCGATGAAACGAAATAATAGACTTTCATCAGTAGACGACGACTTA
GATCTAATGCCATTACCTGATGGTTGTTTAGTAACAAATCATGGACTCGACATTGTAGTT
GTCATCACAAAAACAGATTATATGATCACACTCGAAAAAGAGTTTGATTATAGAGAAGAG
CACTTTGACTTTATGCAGCAATGGATTCGAAGATTTTGTCTTCATTATGGAGCATCATTA
TTTTATACCAGTGTTAAAGAAGATAAAAACTGTGATTTATTATATAAATATTTAACACAT
CGAATCTACGATTTGCCATTTAGAACACCAGCATTAGTTGTGGAAAAAGATGCAGTATTA
ATACCAGCGGGCTGGGACAATCAGAAAAAGATAAGCATATTATATGAAAATATGCACTCA
TGTAAACCAGACGACTTTTTCAATGATATTATCGCTCATCCACCTTCCCGAAAATCTGTG
TCAAATAAAGAAGTCGAGGTTCAAACGGAAGATGAACAAGCATTCTTAGCAAGACAATTG
CAAATTCTTCAACAAGGTGGTGGCCAACAACAACAAACTACAAGATCAGTATCGCCAATG
CGAACGCCTCAACCTGCTGGCAAAGGTGCTCCACGAACGCCAAGTAGTCAAGGTTCTCCA
AATAAAA
>g13727.t2 Gene=g13727 Length=402
METSTQINGLSPAKKKDNAETKENLWSEILGEVQKQGTAKLPSNKCVLVLGDNSSGKTSL
IAKLQGVEDPKKGSGLEYAYIDVRDEYRDDLTRLGVWILDGDIGHLNLLKFALNEKNYAH
TLVILAISMTTPWNWQEQLEHWMKVLGDHLEQLKISSEERQAEKQRLVNLWQTYCETADE
LDPSSPMKRNNRLSSVDDDLDLMPLPDGCLVTNHGLDIVVVITKTDYMITLEKEFDYREE
HFDFMQQWIRRFCLHYGASLFYTSVKEDKNCDLLYKYLTHRIYDLPFRTPALVVEKDAVL
IPAGWDNQKKISILYENMHSCKPDDFFNDIIAHPPSRKSVSNKEVEVQTEDEQAFLARQL
QILQQGGGQQQQTTRSVSPMRTPQPAGKGAPRTPSSQGSPNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13727.t2 | CDD | cd00267 | ABC_ATPase | 40 | 74 | 0.00241856 |
| 4 | g13727.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 5 | g13727.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 360 | 402 | - |
| 6 | g13727.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 360 | 381 | - |
| 2 | g13727.t2 | PANTHER | PTHR12688 | DYNEIN LIGHT INTERMEDIATE CHAIN | 13 | 382 | 3.9E-143 |
| 1 | g13727.t2 | Pfam | PF05783 | Dynein light intermediate chain (DLIC) | 21 | 397 | 2.2E-189 |
| 3 | g13727.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 40 | 284 | 2.25E-13 |
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 transcript has been annotated with K10416 (dynein cytoplasmic 1 light 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.
