General information for g11238.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Clathrin heavy chain.
Parent gene
- The parent gene g11238 is located on chr_1: 14861346..14861913 (- 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_1 | g11238 | g11238.t4 | isoform | g11238.t4 | 14858020 | 14858690 |
| chr_1 | g11238 | g11238.t4 | exon | g11238.t4.exon1 | 14858020 | 14858690 |
| chr_1 | g11238 | g11238.t4 | cds | g11238.t4.CDS1 | 14858022 | 14858534 |
| chr_1 | g11238 | g11238.t4 | TSS | g11238.t4 | NA | NA |
| chr_1 | g11238 | g11238.t4 | TTS | g11238.t4 | NA | NA |
Sequences
>g11238.t4 Gene=g11238 Length=671
CCATCAATTATTTTCACTTTTGCTGTGCGTACACAAACCGGTGGAAAATTGCACATCATC
GAAGTTGGAACACCACCTACAGATAATCAACCGTTTACAAAGAAAACCGTTGATGTTTTC
TTTCCACCTGAAGCGGCTAATGATTTTCCAGTGGCAATGCAAACATCTCAAAAATATGAC
GTCATCTACTTGATTACAAAATATGGGTACATTCATCTTTATGACATTGAAACCGGTACA
TGTATTTACATGAATCGCATTTCTGCCGATACTATTTTTGTAACAGCACCACATGATGCT
AGTGGTGGTATTATTGGTGTTAACCGTAAGGGTCAAGTGTTGTCTGTGACAGTCGATGAG
GAGCAAATTATTCCTTATATTACTACCGTTCTTCAAAATCCAGATTTGGCCTTACGCATG
GCTGTAAGAAACAATTTGAGCGGGGCTGAAGATCTTTTTGTGAGAAAGTTCAATCAACTT
TTCCAAAACGCTCAATATGCTGAAGCCGCAAAAGTTGCAGCCGTCGCTCCAAAGGGAATT
TTGCGTACACCACAAACTATTCAAAAATTCCAACAAGTGCAACCTCCACCGGGCAGCACA
TCACCACCATTGCTTCAATACTTTGGTATTCTCTTAGATCAAGGAAAATTGAATAAATAT
GAATCACTTGA
>g11238.t4 Gene=g11238 Length=171
MQTSQKYDVIYLITKYGYIHLYDIETGTCIYMNRISADTIFVTAPHDASGGIIGVNRKGQ
VLSVTVDEEQIIPYITTVLQNPDLALRMAVRNNLSGAEDLFVRKFNQLFQNAQYAEAAKV
AAVAPKGILRTPQTIQKFQQVQPPPGSTSPPLLQYFGILLDQGKLNKYESL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11238.t4 | Gene3D | G3DSA:2.130.10.110 | - | 1 | 101 | 0e+00 |
| 4 | g11238.t4 | PANTHER | PTHR10292:SF7 | CLATHRIN HEAVY CHAIN 1 | 1 | 171 | 0e+00 |
| 5 | g11238.t4 | PANTHER | PTHR10292 | CLATHRIN HEAVY CHAIN RELATED | 1 | 171 | 0e+00 |
| 2 | g11238.t4 | Pfam | PF01394 | Clathrin propeller repeat | 33 | 67 | 5e-07 |
| 1 | g11238.t4 | Pfam | PF09268 | Clathrin, heavy-chain linker | 68 | 91 | 0e+00 |
| 3 | g11238.t4 | Pfam | PF13838 | Clathrin-H-link | 93 | 159 | 0e+00 |
| 7 | g11238.t4 | SUPERFAMILY | SSF50989 | Clathrin heavy-chain terminal domain | 1 | 67 | 0e+00 |
| 6 | g11238.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 69 | 170 | 0e+00 |
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 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