General information for g4944.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein pelota.
Parent gene
- The parent gene g4944 is located on chr_2: 6131026..6131956 (- 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 | g4944 | g4944.t4 | isoform | g4944.t4 | 6126808 | 6131956 |
| chr_2 | g4944 | g4944.t4 | exon | g4944.t4.exon1 | 6126808 | 6127147 |
| chr_2 | g4944 | g4944.t4 | TTS | g4944.t4 | 6126811 | 6126811 |
| chr_2 | g4944 | g4944.t4 | cds | g4944.t4.CDS1 | 6127047 | 6127147 |
| chr_2 | g4944 | g4944.t4 | exon | g4944.t4.exon2 | 6127241 | 6127347 |
| chr_2 | g4944 | g4944.t4 | cds | g4944.t4.CDS2 | 6127241 | 6127347 |
| chr_2 | g4944 | g4944.t4 | exon | g4944.t4.exon3 | 6130791 | 6131461 |
| chr_2 | g4944 | g4944.t4 | cds | g4944.t4.CDS3 | 6130791 | 6131461 |
| chr_2 | g4944 | g4944.t4 | exon | g4944.t4.exon4 | 6131524 | 6131956 |
| chr_2 | g4944 | g4944.t4 | cds | g4944.t4.CDS4 | 6131524 | 6131571 |
| chr_2 | g4944 | g4944.t4 | TSS | g4944.t4 | 6132074 | 6132074 |
Sequences
>g4944.t4 Gene=g4944 Length=1551
ATGAAGCTCATATTTAAAAATATTGACCGTGGAAGCGGGTAAGTGTAATAATTTAAAAAG
AATAAAAATCGTGTCATAAAATCTTCCACGAAATCATAAACAATAACAAAATTCCTCTAT
TTTTTAGCTCGATCAAAATGCAGCCTGAAGAGGCTGAAGATATGTGGCATGCCTACAATC
TTATTTCAATAGGTGATTTAATCACTGCAAGCACAATTCGAAAAGTAATTTAATAAAATT
TATAAAAATCGTGAATACTTTTAATGAATTTTCTCATATATTTCAGGTCCAAAATGAATC
ATCTACAGGAAGTTCCACATCAAATCGAGTTCGAACCACTTTAACACTTAAGATCGAAAA
TATTGACTATGACACACAGGCTTGCATGCTCAGATTAAAAGGTAGAAACGTAGTGGAAAA
TGATTTTGTTAAGATGGGTGCTTATCACACAATAGATTTAGAATTGAATCGTCCATTTAC
ACTAACAAAACCTGAATGGGACTCAATTGCTCTTGAAAGAGTTGATATGGCATGTGATGT
CACACAAAATGCAGATGTTGCAGCAGTTATCATGCAAGAAGGCATAGCTCACATTTGTTT
AATCACATCAAACATGACTATTGTAAGGAGTAAAATTGATATGGCCATTCCGAGAAAAAG
GAAAAATAATTCATCGCAACATGATAAAGGACTCACAAAGTTTTATGAAGCTGTTATGGA
AGGCATTAAAAGGCACGTAAATTTCGACGTCGTAAAGTGCATTCTCATTGCCTCACCAGC
TTTTGTAAAAGACGCATTCTTTGATTTTATGATTCAAACAGCGACAAGAACTGACCAAAA
AGTCATTCTCGATAACAAGAGTAAATTTATGTTAGTGCATGCATCATCTGGATTTAAGCA
TTCTCTCAAAGAGGTTCTACAAGATCCAGCAGTGCTGGCTAAAATGAGCGATACTAAAGC
AGCTGGCGAAGTGAAACGACTGGAAGCATTTTACACAATGTTACAGTGCGATCCAAATCG
AGCGTTTTATGGTAAAAAACATGTACAGAAGGCGATTGACGCACAGGCTGTTGAAACACT
TTTAATCTCAGATAATTTGTTTCGAAATCAGGATTTAATTCAGCGTAAAGAATATGTTAA
AATGCACGATGATGTACTCGATTCTGGTGGTGATGTAAAAATATTCTCGAGCATGCACGT
GTCTGGTGAACAACTAGCGCAACTGACAGGCATTGCCGCAATTTTGAGATTTCCTATGCC
AGAACTAGAAGACGACGATTCTGAAGAAGATGAAAATTCTGATGCAGATTAAGTTTTGTA
AATAACCGCTTAGAAAAAATAATGAACGATTATCATTCAAGTCATGTGTTCTAAAATATT
ATAACTTTTTTATTATGACAAATATAAAAAGGAGGAAATTAACAATATTTCAGCTTCATG
TTTTTATACGATATTTGCATAAAACAATTCAAATAATTACGCAAGCTAATGATGATAAAC
GAAATTTAACTTTGTGAATTATGATTGCAATAAAAAAATATGAAAATTAAA
>g4944.t4 Gene=g4944 Length=308
MLRLKGRNVVENDFVKMGAYHTIDLELNRPFTLTKPEWDSIALERVDMACDVTQNADVAA
VIMQEGIAHICLITSNMTIVRSKIDMAIPRKRKNNSSQHDKGLTKFYEAVMEGIKRHVNF
DVVKCILIASPAFVKDAFFDFMIQTATRTDQKVILDNKSKFMLVHASSGFKHSLKEVLQD
PAVLAKMSDTKAAGEVKRLEAFYTMLQCDPNRAFYGKKHVQKAIDAQAVETLLISDNLFR
NQDLIQRKEYVKMHDDVLDSGGDVKIFSSMHVSGEQLAQLTGIAAILRFPMPELEDDDSE
EDENSDAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4944.t4 | Gene3D | G3DSA:2.30.30.870 | - | 1 | 53 | 0 |
| 10 | g4944.t4 | Gene3D | G3DSA:3.30.420.60 | - | 57 | 188 | 0 |
| 9 | g4944.t4 | Gene3D | G3DSA:3.30.1330.30 | - | 189 | 306 | 0 |
| 4 | g4944.t4 | PANTHER | PTHR10853 | PELOTA | 1 | 304 | 0 |
| 5 | g4944.t4 | PANTHER | PTHR10853:SF0 | PROTEIN PELOTA HOMOLOG | 1 | 304 | 0 |
| 3 | g4944.t4 | Pfam | PF03463 | eRF1 domain 1 | 1 | 50 | 0 |
| 2 | g4944.t4 | Pfam | PF03464 | eRF1 domain 2 | 57 | 187 | 0 |
| 1 | g4944.t4 | Pfam | PF03465 | eRF1 domain 3 | 193 | 291 | 0 |
| 6 | g4944.t4 | SUPERFAMILY | SSF159065 | Dom34/Pelota N-terminal domain-like | 1 | 51 | 0 |
| 7 | g4944.t4 | SUPERFAMILY | SSF53137 | Translational machinery components | 53 | 192 | 0 |
| 8 | g4944.t4 | SUPERFAMILY | SSF55315 | L30e-like | 186 | 291 | 0 |
| 12 | g4944.t4 | TIGRFAM | TIGR00111 | pelota: mRNA surveillance protein pelota | 2 | 291 | 0 |
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:0070966 | nuclear-transcribed mRNA catabolic process, no-go decay | BP |
| GO:0070481 | nuclear-transcribed mRNA catabolic process, non-stop decay | BP |
| GO:0071025 | RNA surveillance | 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.
