General information for g16405.t18
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.t18 | TSS | g16405.t18 | 9355269 | 9355269 |
| chr_4 | g16405 | g16405.t18 | isoform | g16405.t18 | 9355347 | 9358457 |
| chr_4 | g16405 | g16405.t18 | exon | g16405.t18.exon1 | 9355347 | 9355431 |
| chr_4 | g16405 | g16405.t18 | cds | g16405.t18.CDS1 | 9355347 | 9355431 |
| chr_4 | g16405 | g16405.t18 | exon | g16405.t18.exon2 | 9355495 | 9355539 |
| chr_4 | g16405 | g16405.t18 | cds | g16405.t18.CDS2 | 9355495 | 9355539 |
| chr_4 | g16405 | g16405.t18 | exon | g16405.t18.exon3 | 9355759 | 9355954 |
| chr_4 | g16405 | g16405.t18 | cds | g16405.t18.CDS3 | 9355759 | 9355954 |
| chr_4 | g16405 | g16405.t18 | exon | g16405.t18.exon4 | 9356922 | 9358457 |
| chr_4 | g16405 | g16405.t18 | cds | g16405.t18.CDS4 | 9356922 | 9357108 |
| chr_4 | g16405 | g16405.t18 | TTS | g16405.t18 | 9358435 | 9358435 |
Sequences
>g16405.t18 Gene=g16405 Length=1862
ATGAGTGGTTTAGTTGAAGATTTTTTGGCTCGTGAAAAAGATGGTCTTGCTGGACTTGAA
GATGAAATTCCACAAGCTTTTCAAGAAAATGGAAATTTTAGAGATCAAGATGAGCAGCAT
AACTCATTCACATCAGATCGATCATCATCAACAGAAGTACCTGAAAAGATAAAAAAGTGG
CGTGAGGAACAGCAGTTAAGATTACAAGAAAAAGATGCAGCAGAAGAGAAAGCAAAAGAG
GCACTAAGAAAACAAGCAGAAAAGGAGCTTGAAGATTGGTATAAAAGACATGAGGAGACA
ATTGCTAAGACTAAGACACTTAATAGAAATGCTGAAAAAGAATGTGTAGCAGAAGTGGAA
GAAATGGAACCAGGAACTGAATGGGAACGTATTTCAAAACTCTGTGACTTTGCACAATCA
ACAAAAGCAAGTAAGTCACTCAAAGACAACAGTCGAATGAGAAGCATAATTCTGCAATTA
AAGCAGTCACCACTCGATCGTGAGAAAGCCTAAGTCACCATAAATTGAAAATTTTCCGAT
CTTCATAAAAACTTTTTTGTAGTCGCCATATAAATTTAGTTTTTCTCGTGAGATTCCAAA
AAATGAAAACGATTAAGTGAAGGAAAATTTCACTAGTTAGATTAAGGGAAGAAAAAATTT
TTTTGTGACAAAAAATACAAAGTGTATTAATGTAAAAGTAGAACAAAAATATTCAGGATA
TGAAAAATATGAATCGAAACGATGTGTATTGTGTTGATGTAAGGTAAATATATTTATGAA
AATTTTCTTTCTTGATTTTCAATAGAAATCAATTTATTTTTTAAATAATTAATTATTTTC
AATTTCTTCCAAAAATGGTTTAAAAATTTTCTCTAAAACAAAACACAAAAATCTCATTTT
ATTTTAAGAAATCTCAAAGAAGTTGTGAAAAAATTCAAAGCAGCTATAGAAATAATTTTT
GTTTTATTTATTTTTAAAATTCTCAAATATTTCTATTTTATTAATTTATACTTTTTACTA
ATCAATTTATTTTTAATTAAATCACAAACTAAATCAGATTTTTAATTTTTATAGAATGAA
AATTTAAGAAAATTTCTGTTTCTCATAAATTAATAATGAAATAATAAACTTTTTCGTCTG
ACATGACATGAACAGTTAAAATTCATTTAAATACTCTAAACTATCTTACAGAGTCCGAAA
CCGTTTCACGAATAACTAAAAATAAACTAAATTTTATTCGGTTAAAAATAAAATACTAAC
CGATTAATTTTTAATTGAATAAATTTAGTTAATTTTTAACCGGTTAAATTTAATGGTTTT
TTAGTTTGTTTAATCGGTTAAAATCAACTAAATCAAACAATTTTGACCGGTTAAATTTAT
CAAATTGAAAAGAATGAAAATAAATTTTTTAAATTGATTTTAACCATTTAAACAACAAAA
ATTCAATTAAATTACCCGGTTAAATTTTGAAATAAAAATCAACTAAAATTTAACCGATTA
GTGTTTTATTTTCAACCGAATAAAAGTAGTTGATTTTTAGTTATTTTCAATTTAATTTCA
AACTGTTTTGGACTCTGCTATCTTATAATAAGTCAACACAGAAAATCGAACAAATATTAA
CGAAAACTTAGCAAAGAAAATACAAAGCCATAGCTTTTAGAGAATGAAAAATAGAAACTT
ATGCATTGAATGTTTATAAGAAATGCAAAACTCATCTAATTATTAATTATCAATAAAAAA
TATATTGTATTACTAATAAAAATATAAGAAAAAAAACAAACGAAAAGATATTTGAAGGCT
AAAAATATTAAAAAATAAATGAGAAAAAAATTTTAGAAAATAAATTTTTAGTTTTATTTT
TT
>g16405.t18 Gene=g16405 Length=170
MSGLVEDFLAREKDGLAGLEDEIPQAFQENGNFRDQDEQHNSFTSDRSSSTEVPEKIKKW
REEQQLRLQEKDAAEEKAKEALRKQAEKELEDWYKRHEETIAKTKTLNRNAEKECVAEVE
EMEPGTEWERISKLCDFAQSTKASKSLKDNSRMRSIILQLKQSPLDREKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16405.t18 | Coils | Coil | Coil | 61 | 114 | - |
| 5 | g16405.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 57 | - |
| 2 | g16405.t18 | PANTHER | PTHR10639 | CLATHRIN LIGHT CHAIN | 27 | 164 | 2.3E-27 |
| 3 | g16405.t18 | PANTHER | PTHR10639:SF7 | CLATHRIN LIGHT CHAIN | 27 | 164 | 2.3E-27 |
| 1 | g16405.t18 | Pfam | PF01086 | Clathrin light chain | 31 | 164 | 9.0E-39 |
| 4 | g16405.t18 | ProSitePatterns | PS00581 | Clathrin light chain signature 2. | 148 | 161 | - |
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.
