Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Dynein light chain 1, cytoplasmic.

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 g11819 g11819.t7 isoform g11819.t7 18569496 18578006
chr_1 g11819 g11819.t7 exon g11819.t7.exon1 18569496 18569705
chr_1 g11819 g11819.t7 TSS g11819.t7 18569515 18569515
chr_1 g11819 g11819.t7 exon g11819.t7.exon2 18570012 18570138
chr_1 g11819 g11819.t7 cds g11819.t7.CDS1 18570031 18570138
chr_1 g11819 g11819.t7 exon g11819.t7.exon3 18577378 18577523
chr_1 g11819 g11819.t7 cds g11819.t7.CDS2 18577378 18577523
chr_1 g11819 g11819.t7 exon g11819.t7.exon4 18577643 18578006
chr_1 g11819 g11819.t7 cds g11819.t7.CDS3 18577643 18577712
chr_1 g11819 g11819.t7 TTS g11819.t7 18578010 18578010

Sequences

>g11819.t7 Gene=g11819 Length=847
GCTAGAATTCATCATAGTTTTATAAAAGGTCCCTGCTAGAGTAACCGATTTTTAGAAAGA
AAAAATTAAAGCGAGTGAATATAAAATAAATTCACGGTGAAATAAGTATTAAACCGATCC
AGAAGTCGCATTTAATTACGCTTAATTGATTAAAATTTAAGTGAAAGTTCTCATTTGTAT
TAATTAATTCCAAATTTTTGAGAAAAACAAATCATAAACGGCACAAAACATGAGTGATAG
AAAAGCAGTGATTAAAAATGCTGATATGGGTGAAGAAATGCAACAAGATGCAGTAGATTG
TGCAACTCAAGCACTTGAAAAGTATAACATCGAAAAGGACATTGCTGCATACATAAAAAA
AGAATTTGACAAGAAGTACAATCCTACATGGCATTGCATTGTTGGTCGTAATTTTGGATC
ATACGTCACACATGAGACTCGTCACTTCATATATTTCTATTTGGGACAAGTTGCTATTTT
GCTAATTTCAATGTTGCACAGATGCACTCAAATCAAACTCAAATATTATTTTTTCTATTT
TGTAATATCTTAACATTTTCTGTTCTTCAAATTAAAATAATAAATATTCAATAACCAAAT
GATGTCGATAAAAATAATAGCGATAGGTTTTGGGGACAAACTAAATTTATTTTTAAATTA
ATGAAAAGAATAATTTAAAGGTCAGTTGAAGAGAGATACAGCAAAATTTTTATTTCTCAC
TACCATTCACTTTATTCCTCGTCCTCGTTTTATTTTTATGAAAAAATTCCTAAATAAATG
CATGCTAATTTTTTAAGACACTCTTACACAAATAGAAAAATGAATGAATAAAAATTAAGA
ATATAAA

>g11819.t7 Gene=g11819 Length=107
MSDRKAVIKNADMGEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGR
NFGSYVTHETRHFIYFYLGQVAILLISMLHRCTQIKLKYYFFYFVIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11819.t7 Gene3D G3DSA:3.30.740.10 Protein Inhibitor Of Neuronal Nitric Oxide Synthase; 1 87 6.5E-46
2 g11819.t7 PANTHER PTHR11886:SF62 DYNEIN LIGHT CHAIN 1 86 1.2E-59
3 g11819.t7 PANTHER PTHR11886 DYNEIN LIGHT CHAIN 1 86 1.2E-59
1 g11819.t7 Pfam PF01221 Dynein light chain type 1 5 85 4.7E-40
7 g11819.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 71 -
8 g11819.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 89 -
6 g11819.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 90 107 -
10 g11819.t7 ProSitePatterns PS01239 Dynein light chain type 1 signature. 55 69 -
11 g11819.t7 SMART SM01375 Dynein_light_2 1 88 1.2E-57
4 g11819.t7 SUPERFAMILY SSF54648 DLC 2 85 9.68E-40
9 g11819.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -

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:0030286 dynein complex CC
GO:0005875 microtubule associated complex CC
GO:0007017 microtubule-based process 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.

Raw TPM values