General information for g11835.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein CLP1-like protein.
Parent gene
- The parent gene g11835 is located on chr_1: 18682891..18683563 (- 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 | g11835 | g11835.t3 | isoform | g11835.t3 | 18682014 | 18683563 |
| chr_1 | g11835 | g11835.t3 | exon | g11835.t3.exon1 | 18682014 | 18682202 |
| chr_1 | g11835 | g11835.t3 | TTS | g11835.t3 | 18682026 | 18682026 |
| chr_1 | g11835 | g11835.t3 | exon | g11835.t3.exon2 | 18682262 | 18683170 |
| chr_1 | g11835 | g11835.t3 | cds | g11835.t3.CDS1 | 18682262 | 18683170 |
| chr_1 | g11835 | g11835.t3 | exon | g11835.t3.exon3 | 18683239 | 18683563 |
| chr_1 | g11835 | g11835.t3 | cds | g11835.t3.CDS2 | 18683239 | 18683241 |
| chr_1 | g11835 | g11835.t3 | TSS | g11835.t3 | 18683648 | 18683648 |
Sequences
>g11835.t3 Gene=g11835 Length=1423
ATGACAGAGACAGGAAATTCAAAAGAGTCTAAAGATTATAATTTAGAAAAAGATTGCGAA
CTAAGATTTGAAATTGAAAGCAAATCTCAAATTAAAGTTGAGGTAAATTAAATTTAATAT
TGTAGGTAAATTTTTAATATTTAATATTAATATATTATTTTAGTTGAAATCTGGGTTTGC
AGAGCTTTATGGAACAGAATTGGTAAAATCTAAAAAGTATACGTTTTACCAAGGTGCAAA
AGTGGCAATTTTTACATATCAAGGTTGTGTTATCAACATTTCAGGCTCTCCAGATGTGTG
CTATATCGCACGAGAAACGCCAATGATTCAATATCTTAATACACATAGTGCAATTGAGCA
AATGAGAGTAAATGCTGAAGAAAGAGAAACATGTGGTCCTAAAGTTATGATTGTTGGTCC
AACGGATGTGGGCAAATCAACTTTATGTAAAATCTTATTAAATTATGCTGTTCGACTAGG
ACACAGACCTATCTTATCAGATTTAGATGTTGGACAAGGAAATATATCTATTCCTGGAAC
AATCGCTTCATTATTAATTGAAAGACCAGCATCAATCGAAGAAGGTTTCTTCTCTCAATT
GGCACCTTTAGTAATTCACTATGGTCACAAAACTCCTGATTTTAACAATGAACTTTACAA
AATTTGCATTTCAACACTAGCAGATATAACATTAGAACGTTTAAATGAAGATAAAAGAAC
ATTATCGTCTGGAATTATTATCAACACATGTGGTTGGGTAAAAGGACAAGGGTATCAACA
TTTACTTCACGCTGCAAAAGAATTTAAAGTTGATGTTATTCTCGTATTAGATCAAGAGAG
ACTTTATAATGAATTATTACGAGATGTTGATGCAGGATGTAAAGTAGTTTTTCTGCCAAA
AAGTGGTGGAGTAGTTGAACGTAGTCAACAAACAAGAGCTGAAAGCAGAGATCAAAGGAT
CCGGGAATATTTTTATGGTGTCCCTTTGAGATCACCTTTGTATCCTCATTCTATTGATAT
TAAATTTTCTGATTTGAAACTTTATAAAATTGGCGCGCCTGTTTTGCCTGACTCATGTAT
GCCTCTCGGAATGAAAGCTACTGATAATATGACAAAACTGTGGCCAATTCAACCTGGGCC
ATCTCTAATTCATCACGTACTAGCATTGAGTTTTGCTGAAAATCCTGAACAAGATGTCTT
GAAAAAAAATGTCATAGGTTTCGTTTGTGTGTAAAACAAATGTAGATGTCGAAAGACAAA
CCATAACAGTGCTTTCACCACAGCCCAGACCTTTACCAAATGTTGTTTTACTTTTATCCG
AATTGCAGTTTATTGATAGTCATTGAATTTTTTTTCGATCATTTTATGTCAAAAAAAGAT
TACGTCTGTAATAAATACAATATATTCAAATTCTTATGATGTA
>g11835.t3 Gene=g11835 Length=303
MIQYLNTHSAIEQMRVNAEERETCGPKVMIVGPTDVGKSTLCKILLNYAVRLGHRPILSD
LDVGQGNISIPGTIASLLIERPASIEEGFFSQLAPLVIHYGHKTPDFNNELYKICISTLA
DITLERLNEDKRTLSSGIIINTCGWVKGQGYQHLLHAAKEFKVDVILVLDQERLYNELLR
DVDAGCKVVFLPKSGGVVERSQQTRAESRDQRIREYFYGVPLRSPLYPHSIDIKFSDLKL
YKIGAPVLPDSCMPLGMKATDNMTKLWPIQPGPSLIHHVLALSFAENPEQDVLKKNVIGF
VCV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11835.t3 | CDD | cd01983 | SIMIBI | 26 | 99 | 0.0041128 |
| 6 | g11835.t3 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 223 | 0.0000000 |
| 7 | g11835.t3 | Gene3D | G3DSA:3.30.70.2410 | - | 228 | 303 | 0.0000000 |
| 3 | g11835.t3 | PANTHER | PTHR12755 | CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P | 1 | 303 | 0.0000000 |
| 4 | g11835.t3 | PANTHER | PTHR12755:SF6 | POLYRIBONUCLEOTIDE 5’-HYDROXYL-KINASE CLP1 | 1 | 303 | 0.0000000 |
| 1 | g11835.t3 | Pfam | PF16575 | mRNA cleavage and polyadenylation factor CLP1 P-loop | 32 | 219 | 0.0000000 |
| 2 | g11835.t3 | Pfam | PF06807 | Pre-mRNA cleavage complex II protein Clp1 | 226 | 303 | 0.0000000 |
| 5 | g11835.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 26 | 170 | 0.0000000 |
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:0031124 | mRNA 3’-end processing | 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