General information for g11238.t5
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.t5 | isoform | g11238.t5 | 14858020 | 14861913 |
| chr_1 | g11238 | g11238.t5 | exon | g11238.t5.exon1 | 14858020 | 14859281 |
| chr_1 | g11238 | g11238.t5 | cds | g11238.t5.CDS1 | 14858022 | 14859281 |
| chr_1 | g11238 | g11238.t5 | exon | g11238.t5.exon2 | 14861872 | 14861913 |
| chr_1 | g11238 | g11238.t5 | cds | g11238.t5.CDS2 | 14861872 | 14861913 |
| chr_1 | g11238 | g11238.t5 | TSS | g11238.t5 | NA | NA |
| chr_1 | g11238 | g11238.t5 | TTS | g11238.t5 | NA | NA |
Sequences
>g11238.t5 Gene=g11238 Length=1304
ATGTCTCAGTCATTGCCGATTCGTTTTCAGGAGCATTTGCAGCTCACAAATGTCGGTATT
CAGGCAACATCGATTTCATTTAGTAATCTTACAATGGAATCAGATAAGTTTATCTGCATT
CGAGAAAAAGTTGGAGAAACAGCTCAAGTTGTCATCATTGATATGAGTGATTCTTCAAAT
CCAATTCGACGACCAATTAGCGCTGATTCAGCTATCATGAATCCTGCGAGTAAAGTAATT
GCATTGAAAGCTGCAAAAACTCTTCAAATTTTTAACATCGAGATGAAATCAAAAATGAAG
GCTCACACAATGACTGAGGATGTTGTTTTCTGGAAGTGGATTTCATTAAATACTTTATCA
TTGGTAACTGAAACTTGTGTTTATCATTGGTCAATGGAGGGTGATTCCCAGCCAGTTAAA
ATGTTTGAACGTCATTCGTCACTCAATAGCTGTCAAATCATTAATTATCGCACCGATCCA
AAGCAGCAATGGCTATTACTTATTGGCATTTCAGCACAGCAAAATCGTGTTGTTGGAGCC
ATGCAATTATATTCAGTTGAGAGGAAAGTATCTCAAGCTATTGAAGGTCATGCTGCTGCA
TTTACAACATTCCAGATGGAGGGAAATAAGGAGCCATCAATTATTTTCACTTTTGCTGTG
CGTACACAAACCGGTGGAAAATTGCACATCATCGAAGTTGGAACACCACCTACAGATAAT
CAACCGTTTACAAAGAAAACCGTTGATGTTTTCTTTCCACCTGAAGCGGCTAATGATTTT
CCAGTGGCAATGCAAACATCTCAAAAATATGACGTCATCTACTTGATTACAAAATATGGG
TACATTCATCTTTATGACATTGAAACCGGTACATGTATTTACATGAATCGCATTTCTGCC
GATACTATTTTTGTAACAGCACCACATGATGCTAGTGGTGGTATTATTGGTGTTAACCGT
AAGGGTCAAGTGTTGTCTGTGACAGTCGATGAGGAGCAAATTATTCCTTATATTACTACC
GTTCTTCAAAATCCAGATTTGGCCTTACGCATGGCTGTAAGAAACAATTTGAGCGGGGCT
GAAGATCTTTTTGTGAGAAAGTTCAATCAACTTTTCCAAAACGCTCAATATGCTGAAGCC
GCAAAAGTTGCAGCCGTCGCTCCAAAGGGAATTTTGCGTACACCACAAACTATTCAAAAA
TTCCAACAAGTGCAACCTCCACCGGGCAGCACATCACCACCATTGCTTCAATACTTTGGT
ATTCTCTTAGATCAAGGAAAATTGAATAAATATGAATCACTTGA
>g11238.t5 Gene=g11238 Length=434
MSQSLPIRFQEHLQLTNVGIQATSISFSNLTMESDKFICIREKVGETAQVVIIDMSDSSN
PIRRPISADSAIMNPASKVIALKAAKTLQIFNIEMKSKMKAHTMTEDVVFWKWISLNTLS
LVTETCVYHWSMEGDSQPVKMFERHSSLNSCQIINYRTDPKQQWLLLIGISAQQNRVVGA
MQLYSVERKVSQAIEGHAAAFTTFQMEGNKEPSIIFTFAVRTQTGGKLHIIEVGTPPTDN
QPFTKKTVDVFFPPEAANDFPVAMQTSQKYDVIYLITKYGYIHLYDIETGTCIYMNRISA
DTIFVTAPHDASGGIIGVNRKGQVLSVTVDEEQIIPYITTVLQNPDLALRMAVRNNLSGA
EDLFVRKFNQLFQNAQYAEAAKVAAVAPKGILRTPQTIQKFQQVQPPPGSTSPPLLQYFG
ILLDQGKLNKYESL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11238.t5 | Gene3D | G3DSA:2.130.10.110 | - | 1 | 364 | 0.0e+00 |
| 7 | g11238.t5 | PANTHER | PTHR10292:SF7 | CLATHRIN HEAVY CHAIN 1 | 4 | 434 | 0.0e+00 |
| 8 | g11238.t5 | PANTHER | PTHR10292 | CLATHRIN HEAVY CHAIN RELATED | 4 | 434 | 0.0e+00 |
| 2 | g11238.t5 | Pfam | PF01394 | Clathrin propeller repeat | 20 | 55 | 6.5e-05 |
| 5 | g11238.t5 | Pfam | PF01394 | Clathrin propeller repeat | 149 | 187 | 0.0e+00 |
| 3 | g11238.t5 | Pfam | PF01394 | Clathrin propeller repeat | 257 | 288 | 5.0e-07 |
| 4 | g11238.t5 | Pfam | PF01394 | Clathrin propeller repeat | 296 | 330 | 2.0e-06 |
| 1 | g11238.t5 | Pfam | PF09268 | Clathrin, heavy-chain linker | 331 | 354 | 0.0e+00 |
| 6 | g11238.t5 | Pfam | PF13838 | Clathrin-H-link | 356 | 422 | 0.0e+00 |
| 10 | g11238.t5 | SUPERFAMILY | SSF50989 | Clathrin heavy-chain terminal domain | 4 | 330 | 0.0e+00 |
| 9 | g11238.t5 | SUPERFAMILY | SSF48371 | ARM repeat | 332 | 433 | 0.0e+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