General information for g11835.t10
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.t10 | TTS | g11835.t10 | 18682026 | 18682026 |
| chr_1 | g11835 | g11835.t10 | isoform | g11835.t10 | 18682736 | 18683563 |
| chr_1 | g11835 | g11835.t10 | exon | g11835.t10.exon1 | 18682736 | 18683170 |
| chr_1 | g11835 | g11835.t10 | cds | g11835.t10.CDS1 | 18682736 | 18683170 |
| chr_1 | g11835 | g11835.t10 | exon | g11835.t10.exon2 | 18683239 | 18683400 |
| chr_1 | g11835 | g11835.t10 | cds | g11835.t10.CDS2 | 18683239 | 18683400 |
| chr_1 | g11835 | g11835.t10 | exon | g11835.t10.exon3 | 18683462 | 18683563 |
| chr_1 | g11835 | g11835.t10 | cds | g11835.t10.CDS3 | 18683462 | 18683563 |
| chr_1 | g11835 | g11835.t10 | TSS | g11835.t10 | 18683648 | 18683648 |
Sequences
>g11835.t10 Gene=g11835 Length=699
ATGACAGAGACAGGAAATTCAAAAGAGTCTAAAGATTATAATTTAGAAAAAGATTGCGAA
CTAAGATTTGAAATTGAAAGCAAATCTCAAATTAAAGTTGAGTTGAAATCTGGGTTTGCA
GAGCTTTATGGAACAGAATTGGTAAAATCTAAAAAGTATACGTTTTACCAAGGTGCAAAA
GTGGCAATTTTTACATATCAAGGTTGTGTTATCAACATTTCAGGCTCTCCAGATGTGTGC
TATATCGCACGAGAAACGCCAATGATTCAATATCTTAATACACATAGTGCAATTGAGCAA
ATGAGAGTAAATGCTGAAGAAAGAGAAACATGTGGTCCTAAAGTTATGATTGTTGGTCCA
ACGGATGTGGGCAAATCAACTTTATGTAAAATCTTATTAAATTATGCTGTTCGACTAGGA
CACAGACCTATCTTATCAGATTTAGATGTTGGACAAGGAAATATATCTATTCCTGGAACA
ATCGCTTCATTATTAATTGAAAGACCAGCATCAATCGAAGAAGGTTTCTTCTCTCAATTG
GCACCTTTAGTAATTCACTATGGTCACAAAACTCCTGATTTTAACAATGAACTTTACAAA
ATTTGCATTTCAACACTAGCAGATATAACATTAGAACGTTTAAATGAAGATAAAAGAACA
TTATCGTCTGGAATTATTATCAACACATGTGGTTGGGTA
>g11835.t10 Gene=g11835 Length=233
MTETGNSKESKDYNLEKDCELRFEIESKSQIKVELKSGFAELYGTELVKSKKYTFYQGAK
VAIFTYQGCVINISGSPDVCYIARETPMIQYLNTHSAIEQMRVNAEERETCGPKVMIVGP
TDVGKSTLCKILLNYAVRLGHRPILSDLDVGQGNISIPGTIASLLIERPASIEEGFFSQL
APLVIHYGHKTPDFNNELYKICISTLADITLERLNEDKRTLSSGIIINTCGWV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11835.t10 | CDD | cd01983 | SIMIBI | 113 | 186 | 0.0026626 |
| 7 | g11835.t10 | Gene3D | G3DSA:2.60.120.1030 | - | 3 | 86 | 0.0000000 |
| 6 | g11835.t10 | Gene3D | G3DSA:3.40.50.300 | - | 87 | 233 | 0.0000000 |
| 3 | g11835.t10 | PANTHER | PTHR12755 | CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P | 7 | 233 | 0.0000000 |
| 4 | g11835.t10 | PANTHER | PTHR12755:SF6 | POLYRIBONUCLEOTIDE 5’-HYDROXYL-KINASE CLP1 | 7 | 233 | 0.0000000 |
| 1 | g11835.t10 | Pfam | PF16573 | N-terminal beta-sandwich domain of polyadenylation factor | 15 | 105 | 0.0000000 |
| 2 | g11835.t10 | Pfam | PF16575 | mRNA cleavage and polyadenylation factor CLP1 P-loop | 119 | 233 | 0.0000000 |
| 5 | g11835.t10 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 113 | 166 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
