General information for g8479.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable RNA 3’-terminal phosphate cyclase-like protein.
Parent gene
- The parent gene g8479 is located on chr_2: 30901458..30902301 (+ 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_2 | g8479 | g8479.t2 | TSS | g8479.t2 | 30901061 | 30901061 |
| chr_2 | g8479 | g8479.t2 | isoform | g8479.t2 | 30901458 | 30902301 |
| chr_2 | g8479 | g8479.t2 | exon | g8479.t2.exon1 | 30901458 | 30902301 |
| chr_2 | g8479 | g8479.t2 | cds | g8479.t2.CDS1 | 30901600 | 30902301 |
| chr_2 | g8479 | g8479.t2 | TTS | g8479.t2 | 30902384 | 30902384 |
Sequences
>g8479.t2 Gene=g8479 Length=844
AATTTTTGTAGGATATTATCTTGACGTATTAATTGCTTTTGGTCCATTCTGCAAATTTCC
AATTGATGCTAAATTAAAAGGAGTTACAAATAGTTTTGATAGTCCATCAGTTGATCATAT
ACGATCATCAGCATTTAATATTATGAAACGTTTTATTATTGAAGAAGATGCTTTTGAATT
AAAAATTCTAAAACGTGGAATGATGCCAGATGGTGGTGGAGAAATTTCATTTAAGATCAA
ACCAGTACTTAAATTGCGAGCTCTACAACTTGTAAAAACCGGCATGGTGAAGAGAATCAG
AGGAACAGTTTATTCATGCAAAGTATCACCAACTTTTTCAAATCGAACAATTGAATCCGC
AAAAGGAATTATGCTAAATTTCATTCCTGATGTCTATCTTCATACAGATCAACATAAGGG
CAAATCAAGTGGACTTTCACCTGGATATGGAGTAATTCTAAATGCTGAAACTACTGAGAA
TGTAATCTTTTCAACTGAAATCGTAAATATGGAAAAAGGAATTTTGCCCGAAGACGTAGG
AAAGTTTTGCGCTAACAAATTACTTGATGAGATTTATCGTGGAGGCTGTTGTGATAGTAC
ATTTCAATGGTTGATGATGCTCTATATGGCATTAGGCCCAAAAAGTGTTTCTAAAGTTGT
TACTGGCCCATTTTCTCGTCACACTGTTACATATTTGCAATTAATAAAGGAAATACTTGG
AGTTAAATTTAAAATAGAAAGCTATGAGGAAGAAGAAGATGATGAAGATGATTCACAGTG
TTATAAAGTAATGGTCGCTTGTGTAGGACTTGGATATACAAACTTGGCAAAGAGAGCTTT
ATAA
>g8479.t2 Gene=g8479 Length=233
MKRFIIEEDAFELKILKRGMMPDGGGEISFKIKPVLKLRALQLVKTGMVKRIRGTVYSCK
VSPTFSNRTIESAKGIMLNFIPDVYLHTDQHKGKSSGLSPGYGVILNAETTENVIFSTEI
VNMEKGILPEDVGKFCANKLLDEIYRGGCCDSTFQWLMMLYMALGPKSVSKVVTGPFSRH
TVTYLQLIKEILGVKFKIESYEEEEDDEDDSQCYKVMVACVGLGYTNLAKRAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8479.t2 | Gene3D | G3DSA:3.30.360.20 | - | 45 | 141 | 6.5E-36 |
| 3 | g8479.t2 | PANTHER | PTHR11096 | RNA 3’ TERMINAL PHOSPHATE CYCLASE | 1 | 231 | 4.9E-74 |
| 4 | g8479.t2 | PANTHER | PTHR11096:SF1 | RNA 3’-TERMINAL PHOSPHATE CYCLASE-LIKE PROTEIN | 1 | 231 | 4.9E-74 |
| 2 | g8479.t2 | Pfam | PF01137 | RNA 3’-terminal phosphate cyclase | 2 | 198 | 3.8E-19 |
| 1 | g8479.t2 | Pfam | PF05189 | RNA 3’-terminal phosphate cyclase (RTC), insert domain | 45 | 144 | 2.8E-30 |
| 6 | g8479.t2 | ProSitePatterns | PS01287 | RNA 3’-terminal phosphate cyclase signature. | 18 | 28 | - |
| 5 | g8479.t2 | SUPERFAMILY | SSF55205 | EPT/RTPC-like | 2 | 95 | 5.49E-14 |
| 8 | g8479.t2 | TIGRFAM | TIGR03400 | 18S_RNA_Rcl1p: 18S rRNA biogenesis protein RCL1 | 1 | 231 | 1.9E-81 |
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:0006396 | RNA processing | BP |
| GO:0042254 | ribosome biogenesis | BP |
| GO:0005730 | nucleolus | CC |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11108 (RNA 3’-terminal phosphate cyclase-like protein)
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.
