General information for g11835.t9
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.t9 | TTS | g11835.t9 | 18682026 | 18682026 |
| chr_1 | g11835 | g11835.t9 | isoform | g11835.t9 | 18682091 | 18683563 |
| chr_1 | g11835 | g11835.t9 | exon | g11835.t9.exon1 | 18682091 | 18682202 |
| chr_1 | g11835 | g11835.t9 | cds | g11835.t9.CDS1 | 18682101 | 18682202 |
| chr_1 | g11835 | g11835.t9 | exon | g11835.t9.exon2 | 18682268 | 18683170 |
| chr_1 | g11835 | g11835.t9 | cds | g11835.t9.CDS2 | 18682268 | 18683170 |
| chr_1 | g11835 | g11835.t9 | exon | g11835.t9.exon3 | 18683239 | 18683400 |
| chr_1 | g11835 | g11835.t9 | cds | g11835.t9.CDS3 | 18683239 | 18683400 |
| chr_1 | g11835 | g11835.t9 | exon | g11835.t9.exon4 | 18683462 | 18683563 |
| chr_1 | g11835 | g11835.t9 | cds | g11835.t9.CDS4 | 18683462 | 18683563 |
| chr_1 | g11835 | g11835.t9 | TSS | g11835.t9 | 18683648 | 18683648 |
Sequences
>g11835.t9 Gene=g11835 Length=1279
ATGACAGAGACAGGAAATTCAAAAGAGTCTAAAGATTATAATTTAGAAAAAGATTGCGAA
CTAAGATTTGAAATTGAAAGCAAATCTCAAATTAAAGTTGAGTTGAAATCTGGGTTTGCA
GAGCTTTATGGAACAGAATTGGTAAAATCTAAAAAGTATACGTTTTACCAAGGTGCAAAA
GTGGCAATTTTTACATATCAAGGTTGTGTTATCAACATTTCAGGCTCTCCAGATGTGTGC
TATATCGCACGAGAAACGCCAATGATTCAATATCTTAATACACATAGTGCAATTGAGCAA
ATGAGAGTAAATGCTGAAGAAAGAGAAACATGTGGTCCTAAAGTTATGATTGTTGGTCCA
ACGGATGTGGGCAAATCAACTTTATGTAAAATCTTATTAAATTATGCTGTTCGACTAGGA
CACAGACCTATCTTATCAGATTTAGATGTTGGACAAGGAAATATATCTATTCCTGGAACA
ATCGCTTCATTATTAATTGAAAGACCAGCATCAATCGAAGAAGGTTTCTTCTCTCAATTG
GCACCTTTAGTAATTCACTATGGTCACAAAACTCCTGATTTTAACAATGAACTTTACAAA
ATTTGCATTTCAACACTAGCAGATATAACATTAGAACGTTTAAATGAAGATAAAAGAACA
TTATCGTCTGGAATTATTATCAACACATGTGGTTGGGTAAAAGGACAAGGGTATCAACAT
TTACTTCACGCTGCAAAAGAATTTAAAGTTGATGTTATTCTCGTATTAGATCAAGAGAGA
CTTTATAATGAATTATTACGAGATGTTGATGCAGGATGTAAAGTAGTTTTTCTGCCAAAA
AGTGGTGGAGTAGTTGAACGTAGTCAACAAACAAGAGCTGAAAGCAGAGATCAAAGGATC
CGGGAATATTTTTATGGTGTCCCTTTGAGATCACCTTTGTATCCTCATTCTATTGATATT
AAATTTTCTGATTTGAAACTTTATAAAATTGGCGCGCCTGTTTTGCCTGACTCATGTATG
CCTCTCGGAATGAAAGCTACTGATAATATGACAAAACTGTGGCCAATTCAACCTGGGCCA
TCTCTAATTCATCACGTACTAGCATTGAGTTTTGCTGAAAATCCTGAACAAGATGTCTTG
AAAAAAAATGTCATAGGTTTCGTTTGTAACAAATGTAGATGTCGAAAGACAAACCATAAC
AGTGCTTTCACCACAGCCCAGACCTTTACCAAATGTTGTTTTACTTTTATCCGAATTGCA
GTTTATTGATAGTCATTGA
>g11835.t9 Gene=g11835 Length=422
MTETGNSKESKDYNLEKDCELRFEIESKSQIKVELKSGFAELYGTELVKSKKYTFYQGAK
VAIFTYQGCVINISGSPDVCYIARETPMIQYLNTHSAIEQMRVNAEERETCGPKVMIVGP
TDVGKSTLCKILLNYAVRLGHRPILSDLDVGQGNISIPGTIASLLIERPASIEEGFFSQL
APLVIHYGHKTPDFNNELYKICISTLADITLERLNEDKRTLSSGIIINTCGWVKGQGYQH
LLHAAKEFKVDVILVLDQERLYNELLRDVDAGCKVVFLPKSGGVVERSQQTRAESRDQRI
REYFYGVPLRSPLYPHSIDIKFSDLKLYKIGAPVLPDSCMPLGMKATDNMTKLWPIQPGP
SLIHHVLALSFAENPEQDVLKKNVIGFVCNKCRCRKTNHNSAFTTAQTFTKCCFTFIRIA
VY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g11835.t9 | CDD | cd01983 | SIMIBI | 113 | 186 | 0.0033145 |
| 10 | g11835.t9 | Gene3D | G3DSA:2.60.120.1030 | - | 4 | 86 | 0.0000000 |
| 8 | g11835.t9 | Gene3D | G3DSA:3.40.50.300 | - | 87 | 310 | 0.0000000 |
| 9 | g11835.t9 | Gene3D | G3DSA:3.30.70.2410 | - | 315 | 391 | 0.0000000 |
| 6 | g11835.t9 | Hamap | MF_03035 | Polyribonucleotide 5’-hydroxyl-kinase Clp1 [CLP1]. | 10 | 421 | 25.5894850 |
| 4 | g11835.t9 | PANTHER | PTHR12755 | CLEAVAGE/POLYADENYLATION FACTOR IA SUBUNIT CLP1P | 7 | 389 | 0.0000000 |
| 5 | g11835.t9 | PANTHER | PTHR12755:SF6 | POLYRIBONUCLEOTIDE 5’-HYDROXYL-KINASE CLP1 | 7 | 389 | 0.0000000 |
| 1 | g11835.t9 | Pfam | PF16573 | N-terminal beta-sandwich domain of polyadenylation factor | 15 | 105 | 0.0000000 |
| 2 | g11835.t9 | Pfam | PF16575 | mRNA cleavage and polyadenylation factor CLP1 P-loop | 119 | 306 | 0.0000000 |
| 3 | g11835.t9 | Pfam | PF06807 | Pre-mRNA cleavage complex II protein Clp1 | 313 | 389 | 0.0000000 |
| 7 | g11835.t9 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 113 | 257 | 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 |
| GO:0005849 | mRNA cleavage factor complex | CC |
KEGG
Orthology
- This transcript has been annotated with K14399 (polyribonucleotide 5’-hydroxyl-kinase)
Pathway
- This transcript belongs to the following pathways
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.
