Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytoplasmic dynein 1 light intermediate chain 1.

Parent gene

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.t3 TSS g13727.t3 32084330 32084330
chr_1 g13727 g13727.t3 isoform g13727.t3 32084421 32095357
chr_1 g13727 g13727.t3 exon g13727.t3.exon1 32084421 32084497
chr_1 g13727 g13727.t3 cds g13727.t3.CDS1 32084421 32084497
chr_1 g13727 g13727.t3 exon g13727.t3.exon2 32084967 32085157
chr_1 g13727 g13727.t3 cds g13727.t3.CDS2 32084967 32085157
chr_1 g13727 g13727.t3 exon g13727.t3.exon3 32085216 32085758
chr_1 g13727 g13727.t3 cds g13727.t3.CDS3 32085216 32085758
chr_1 g13727 g13727.t3 exon g13727.t3.exon4 32095135 32095357
chr_1 g13727 g13727.t3 cds g13727.t3.CDS4 32095135 32095154
chr_1 g13727 g13727.t3 TTS g13727.t3 NA NA

Sequences

>g13727.t3 Gene=g13727 Length=1034
ATGGAGACTTCAACACAAATAAATGGACTCTCACCTGCAAAAAAGAAGGATAATGCAGAA
ACAAAGGAGAATTTATGGTCAGAAATTCTTGGTGAAGTTCAAAAACAAGGCACAGCTAAA
TTACCGTCAAATAAATGTGTGTTAGTACTAGGAGACAACTCATCTGGGAAAACGTCACTT
ATTGCAAAATTGCAAGGTGTAGAAGATCCTAAAAAAGGTTCTGGATTAGAATATGCATAC
ATTGATGTGAGGGATGAATATCGAGATGATCTAACACGACTTGGTGTGTGGATTTTAGAC
GGTGATATTGGACATCTGAATCTCTTAAAATTTGCACTTAACGAGAAAAATTACGCTCAC
ACACTGGTTATACTTGCAATTTCAATGACGACACCTTGGAATTGGCAAGAACAACTCGAA
CATTGGATGAAAGTTCTTGGGGATCATTTAGAACAATTAAAAATATCATCTGAAGAACGT
CAAGCTGAGAAGCAGCGATTAGTAAATTTGTGGCAAACTTATTGTGAAACTGCCGATGAA
CTTGATCCCAGCTCACCGATGAAACGAAATAATAGACTTTCATCAGTAGACGACGACTTA
GATCTAATGCCATTACCTGATGGTTGTTTAGTAACAAATCATGGACTCGACATTGTAGTT
GTCATCACAAAAACAGATTATATGATCACACTCGAAAAAGAGTTTGATTATAGAGAAGAG
CACTTTGACTTTATGCAGCAATGGATTCGAAGATTTTGTCTTCATTATGGAGCATCATTA
TTTTATACCAGTGTTAAAGAAGATAAAAACTATTGTATTGTAAATATTTAAAACTTGTTA
GATGAATGAGAATATAATGATGAATGCAACAAAATGTAAAATGCAAAAACATGATGATAA
AAAGCTAAATTGACTTTAATAAAAAGTGAATAAAAAATTTAAATTGACAATATTTTATTT
TATTTAGAACACATTTTTTATTGTTTCAGTTTGATGCTTTTTCAATATTTACAGATCTCA
AATATTGACATTAT

>g13727.t3 Gene=g13727 Length=276
METSTQINGLSPAKKKDNAETKENLWSEILGEVQKQGTAKLPSNKCVLVLGDNSSGKTSL
IAKLQGVEDPKKGSGLEYAYIDVRDEYRDDLTRLGVWILDGDIGHLNLLKFALNEKNYAH
TLVILAISMTTPWNWQEQLEHWMKVLGDHLEQLKISSEERQAEKQRLVNLWQTYCETADE
LDPSSPMKRNNRLSSVDDDLDLMPLPDGCLVTNHGLDIVVVITKTDYMITLEKEFDYREE
HFDFMQQWIRRFCLHYGASLFYTSVKEDKNYCIVNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g13727.t3 CDD cd00267 ABC_ATPase 40 74 0.00166355
4 g13727.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
2 g13727.t3 PANTHER PTHR12688 DYNEIN LIGHT INTERMEDIATE CHAIN 13 272 2.3E-98
1 g13727.t3 Pfam PF05783 Dynein light intermediate chain (DLIC) 21 272 1.8E-128
3 g13727.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 40 271 4.94E-11

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. There were no conditions that were differentially expressed