Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Cytoplasmic dynein 2 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_2 g6628 g6628.t1 isoform g6628.t1 17866702 17867826
chr_2 g6628 g6628.t1 exon g6628.t1.exon1 17866702 17867643
chr_2 g6628 g6628.t1 cds g6628.t1.CDS1 17866702 17867643
chr_2 g6628 g6628.t1 exon g6628.t1.exon2 17867704 17867826
chr_2 g6628 g6628.t1 cds g6628.t1.CDS2 17867704 17867826
chr_2 g6628 g6628.t1 TSS g6628.t1 NA NA
chr_2 g6628 g6628.t1 TTS g6628.t1 NA NA

Sequences

>g6628.t1 Gene=g6628 Length=1065
ATGTCTGAAGTAGAGACAATTCAAGAAATTGCTTTTAAATTAATGTTAGAGCAAAATAAG
AATGATAAGATTCTTAACGGTACAACAGAGAAAACAATTTTTGTGCTTGGTTCTAAAGGA
GTGGGAAAATCAACAATGATTAATAATTTTCTTGACAAAAATGAGCCATTACGTACAACT
CCAACATTAGCAATTGAATATTCCTATGCAAAAAGAACAAATTCAAATGGACAATCAAAT
CAAAAGTTAATTGGAAATATTTGGGAGTTGGGTAGTTTAGCAAATTCAAATCAATTAATT
GATGTACCCATAAAATCACATGGTTCACTTGAAAATTTTTCAGCTGTAATTATGTTAAAT
TTAGCAGAACCTGATAAAATTTCTTTAGACCTTGAAGCGGCATTGCAAGGCCTTAAAAAT
TCATTTTCAAATAATTTCAATGATTCCGAAATACGTCAATTTAGAGAAAAAATTATTGAA
AATGAAGCATATAAAAATCATCCCGACATACAAACATTGGAAATTATGCCTTGTCAAGTG
GTTATTCTAGGCGGAATGTATGATCAATTTGAAAATCTAAATTCAGAGATAAAACGACAT
GTGATTAAGTTTTTGCGCTCCATCAGTCACACAATTGGTTCATCACTTATATTTTACTCA
TCGAAAATTCCATCTTTAGCAAAAACAGTTAGAGATATTATGAGTAAACTAGCGTTTAAT
TCTCCACTAAATCCAATTCGTATTCAAAGAATTGATTATAATGAACCAATTATGATTAAT
GCTTTGAGTGATACTTGGGAAAAAATTGGTGTAATGCCAAGTAATAGTGAACGCATCAGT
ATTCATTATAATACACAAATTAAACAAAATAAAAAAACAAATGATAACAGCTTAAAAGAA
GTGGTAACTAATCCTACAAATGACGTCAATTTTCGCGAAGCAATAATTGATGATCTTCGA
GCCATGAAGGACGAAGAGTTATTGAGGTTGATCAAACACTCTGACGTAAAAATCAAATTT
GATTCATTTAATCTTACGAATAGTCCATTTAATTATCTAAATTAA

>g6628.t1 Gene=g6628 Length=354
MSEVETIQEIAFKLMLEQNKNDKILNGTTEKTIFVLGSKGVGKSTMINNFLDKNEPLRTT
PTLAIEYSYAKRTNSNGQSNQKLIGNIWELGSLANSNQLIDVPIKSHGSLENFSAVIMLN
LAEPDKISLDLEAALQGLKNSFSNNFNDSEIRQFREKIIENEAYKNHPDIQTLEIMPCQV
VILGGMYDQFENLNSEIKRHVIKFLRSISHTIGSSLIFYSSKIPSLAKTVRDIMSKLAFN
SPLNPIRIQRIDYNEPIMINALSDTWEKIGVMPSNSERISIHYNTQIKQNKKTNDNSLKE
VVTNPTNDVNFREAIIDDLRAMKDEELLRLIKHSDVKIKFDSFNLTNSPFNYLN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g6628.t1 Gene3D G3DSA:3.40.50.300 - 27 223 1.4e-05
1 g6628.t1 PANTHER PTHR13236 DYNEIN 2 LIGHT INTERMEDIATE CHAIN, ISOFORM 2 6 340 0.0e+00
2 g6628.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 30 117 1.0e-07

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:0005868 cytoplasmic dynein complex CC
GO:0035735 intraciliary transport involved in cilium assembly BP
GO:0035721 intraciliary retrograde transport BP

KEGG

Orthology

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. There were no conditions that were differentially expressed