Gene loci information

Transcript annotation

  • This transcript has been annotated as Clathrin heavy chain.

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 g11238 g11238.t3 TTS g11238.t3 14853234 14853234
chr_1 g11238 g11238.t3 isoform g11238.t3 14854114 14855211
chr_1 g11238 g11238.t3 exon g11238.t3.exon1 14854114 14854336
chr_1 g11238 g11238.t3 cds g11238.t3.CDS1 14854115 14854336
chr_1 g11238 g11238.t3 exon g11238.t3.exon2 14854390 14854476
chr_1 g11238 g11238.t3 cds g11238.t3.CDS2 14854390 14854476
chr_1 g11238 g11238.t3 exon g11238.t3.exon3 14854539 14854705
chr_1 g11238 g11238.t3 cds g11238.t3.CDS3 14854539 14854705
chr_1 g11238 g11238.t3 exon g11238.t3.exon4 14854772 14855211
chr_1 g11238 g11238.t3 cds g11238.t3.CDS4 14854772 14855189
chr_1 g11238 g11238.t3 TSS g11238.t3 NA NA

Sequences

>g11238.t3 Gene=g11238 Length=917
ATACGATAATGCAGTGTTAGCAATGATGGCACATCCAACTGAAGCTTGGCGTGAAGGGCA
CTTTAAAGATATTATCACAAAAGTGGCAAACATTGAGCTCTACTATAAAGCAATCCAATT
CTACTTGGATTATAAACCACTCTTATTGAATGACCTGCTTTTAGTTCTTACTCCACGTAT
GGATCATACTAGATCTGTCAACTTTTTCACAAAAACTGGACATCTTCAACTCGTCAAACC
TTACTTGCGATCAGTTCAAAGTTTGAATAACAAAGCCATTAATGAGGCACTAAATGGACT
TTTAATCGACGAAGAAGACTACCAAGGATTGAGGACATCAATTGATGCATTCGACAACTT
TGACAACATTGCATTAGCACAGAAACTTGAGAAACACGAATTAACAGAATTCCGTCGTAT
TGCTGCTTATCTATACAAAGGTAACAATCGCTGGAAGCAAAGTGTTGAATTATGTAAGAA
AGATCGCCTATTCAAAGACGCAATGGAATATGCAGCTGAATCACACCAACAGGAAATTGC
TGAAGAACTTTTGCAGTGGTTCCTTGAACGTGGCGCTAAAGATTGTTTCGCTGCATGCCT
CTATACTTGCTATGATCTTTTAAGACCTGATGTTATTCTCGAATTAGCATGGAGACACAA
TATTATGGACTTTGCAATGCCCTTCATGATCAATGTGATAAGGGAATATACAACAAAAGT
AGATAAACTTGAAGCAGCAAATGCCGAAAGAGAGAAAGAGGGTGAAAATACAGAGCATAA
GCCAATAATTATGCAGGAACCACAATTGATGTTGACAGCAGGTCCTGCTTATCAATATGG
TGCTCCTCAATACGCTCCAAATATTCCAAATATGCCATATGGAGCAGCGCCGCCAGCGAA
TCCATACCAAAACTATG

>g11238.t3 Gene=g11238 Length=298
MMAHPTEAWREGHFKDIITKVANIELYYKAIQFYLDYKPLLLNDLLLVLTPRMDHTRSVN
FFTKTGHLQLVKPYLRSVQSLNNKAINEALNGLLIDEEDYQGLRTSIDAFDNFDNIALAQ
KLEKHELTEFRRIAAYLYKGNNRWKQSVELCKKDRLFKDAMEYAAESHQQEIAEELLQWF
LERGAKDCFAACLYTCYDLLRPDVILELAWRHNIMDFAMPFMINVIREYTTKVDKLEAAN
AEREKEGENTEHKPIIMQEPQLMLTAGPAYQYGAPQYAPNIPNMPYGAAPPANPYQNY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11238.t3 Coils Coil Coil 226 253 -
6 g11238.t3 Gene3D G3DSA:1.25.40.10 - 1 145 7.9E-69
7 g11238.t3 Gene3D G3DSA:1.25.40.730 - 151 247 1.7E-45
2 g11238.t3 PANTHER PTHR10292:SF7 CLATHRIN HEAVY CHAIN 1 1 273 1.1E-141
3 g11238.t3 PANTHER PTHR10292 CLATHRIN HEAVY CHAIN RELATED 1 273 1.1E-141
1 g11238.t3 Pfam PF00637 Region in Clathrin and VPS 48 186 1.1E-30
10 g11238.t3 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 1 43 10.432
9 g11238.t3 ProSiteProfiles PS50236 Clathrin heavy-chain (CHCR) repeat profile. 46 189 36.09
5 g11238.t3 SMART SM00299 CLH_2 46 205 2.8E-39
4 g11238.t3 SUPERFAMILY SSF48371 ARM repeat 1 139 1.21E-40

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:0005515 protein binding 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.

Raw TPM values