General information for g16405.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Clathrin light chain.
Parent gene
- The parent gene g16405 is located on chr_4: 9356918..9358457 (+ 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_4 | g16405 | g16405.t1 | TSS | g16405.t1 | 9355269 | 9355269 |
| chr_4 | g16405 | g16405.t1 | isoform | g16405.t1 | 9355347 | 9357108 |
| chr_4 | g16405 | g16405.t1 | exon | g16405.t1.exon1 | 9355347 | 9355431 |
| chr_4 | g16405 | g16405.t1 | cds | g16405.t1.CDS1 | 9355347 | 9355431 |
| chr_4 | g16405 | g16405.t1 | exon | g16405.t1.exon2 | 9355495 | 9355545 |
| chr_4 | g16405 | g16405.t1 | cds | g16405.t1.CDS2 | 9355495 | 9355545 |
| chr_4 | g16405 | g16405.t1 | exon | g16405.t1.exon3 | 9355759 | 9355954 |
| chr_4 | g16405 | g16405.t1 | cds | g16405.t1.CDS3 | 9355759 | 9355954 |
| chr_4 | g16405 | g16405.t1 | exon | g16405.t1.exon4 | 9356922 | 9357108 |
| chr_4 | g16405 | g16405.t1 | cds | g16405.t1.CDS4 | 9356922 | 9357108 |
| chr_4 | g16405 | g16405.t1 | TTS | g16405.t1 | 9357192 | 9357192 |
Sequences
>g16405.t1 Gene=g16405 Length=519
ATGAGTGGTTTAGTTGAAGATTTTTTGGCTCGTGAAAAAGATGGTCTTGCTGGACTTGAA
GATGAAATTCCACAAGCTTTTCAAGAAAATGGAAATTTTAGAGATCAAGATGAGCAGCAT
AACTCATTCAGTAATGCATCAGATCGATCATCATCAACAGAAGTACCTGAAAAGATAAAA
AAGTGGCGTGAGGAACAGCAGTTAAGATTACAAGAAAAAGATGCAGCAGAAGAGAAAGCA
AAAGAGGCACTAAGAAAACAAGCAGAAAAGGAGCTTGAAGATTGGTATAAAAGACATGAG
GAGACAATTGCTAAGACTAAGACACTTAATAGAAATGCTGAAAAAGAATGTGTAGCAGAA
GTGGAAGAAATGGAACCAGGAACTGAATGGGAACGTATTTCAAAACTCTGTGACTTTGCA
CAATCAACAAAAGCAAGTAAGTCACTCAAAGACAACAGTCGAATGAGAAGCATAATTCTG
CAATTAAAGCAGTCACCACTCGATCGTGAGAAAGCCTAA
>g16405.t1 Gene=g16405 Length=172
MSGLVEDFLAREKDGLAGLEDEIPQAFQENGNFRDQDEQHNSFSNASDRSSSTEVPEKIK
KWREEQQLRLQEKDAAEEKAKEALRKQAEKELEDWYKRHEETIAKTKTLNRNAEKECVAE
VEEMEPGTEWERISKLCDFAQSTKASKSLKDNSRMRSIILQLKQSPLDREKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g16405.t1 | Coils | Coil | Coil | 63 | 116 | - |
| 8 | g16405.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 59 | - |
| 7 | g16405.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 29 | 52 | - |
| 3 | g16405.t1 | PANTHER | PTHR10639 | CLATHRIN LIGHT CHAIN | 30 | 114 | 6.1E-27 |
| 5 | g16405.t1 | PANTHER | PTHR10639:SF1 | CLATHRIN LIGHT CHAIN A | 30 | 114 | 6.1E-27 |
| 2 | g16405.t1 | PANTHER | PTHR10639 | CLATHRIN LIGHT CHAIN | 113 | 167 | 6.1E-27 |
| 4 | g16405.t1 | PANTHER | PTHR10639:SF1 | CLATHRIN LIGHT CHAIN A | 113 | 167 | 6.1E-27 |
| 1 | g16405.t1 | Pfam | PF01086 | Clathrin light chain | 35 | 166 | 1.2E-38 |
| 6 | g16405.t1 | ProSitePatterns | PS00581 | Clathrin light chain signature 2. | 150 | 163 | - |
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:0006886 | intracellular protein transport | BP |
| GO:0030132 | clathrin coat of coated pit | CC |
| GO:0030130 | clathrin coat of trans-Golgi network vesicle | CC |
| GO:0005198 | structural molecule activity | MF |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K04644 (clathrin light chain A)
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.
