General information for g4944.t2
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.t2 | isoform | g4944.t2 | 6120665 | 6131956 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon1 | 6120665 | 6120674 |
| chr_2 | g4944 | g4944.t2 | TTS | g4944.t2 | 6120671 | 6120671 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon2 | 6126806 | 6127147 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS1 | 6127047 | 6127147 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon3 | 6127241 | 6127347 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS2 | 6127241 | 6127347 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon4 | 6130791 | 6131461 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS3 | 6130791 | 6131461 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon5 | 6131524 | 6131670 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS4 | 6131524 | 6131670 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon6 | 6131733 | 6131829 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS5 | 6131733 | 6131829 |
| chr_2 | g4944 | g4944.t2 | exon | g4944.t2.exon7 | 6131919 | 6131956 |
| chr_2 | g4944 | g4944.t2 | cds | g4944.t2.CDS6 | 6131919 | 6131956 |
| chr_2 | g4944 | g4944.t2 | TSS | g4944.t2 | 6132074 | 6132074 |
Sequences
>g4944.t2 Gene=g4944 Length=1412
ATGAAGCTCATATTTAAAAATATTGACCGTGGAAGCGGCTCGATCAAAATGCAGCCTGAA
GAGGCTGAAGATATGTGGCATGCCTACAATCTTATTTCAATAGGTGATTTAATCACTGCA
AGCACAATTCGAAAAGTCCAAAATGAATCATCTACAGGAAGTTCCACATCAAATCGAGTT
CGAACCACTTTAACACTTAAGATCGAAAATATTGACTATGACACACAGGCTTGCATGCTC
AGATTAAAAGGTAGAAACGTAGTGGAAAATGATTTTGTTAAGATGGGTGCTTATCACACA
ATAGATTTAGAATTGAATCGTCCATTTACACTAACAAAACCTGAATGGGACTCAATTGCT
CTTGAAAGAGTTGATATGGCATGTGATGTCACACAAAATGCAGATGTTGCAGCAGTTATC
ATGCAAGAAGGCATAGCTCACATTTGTTTAATCACATCAAACATGACTATTGTAAGGAGT
AAAATTGATATGGCCATTCCGAGAAAAAGGAAAAATAATTCATCGCAACATGATAAAGGA
CTCACAAAGTTTTATGAAGCTGTTATGGAAGGCATTAAAAGGCACGTAAATTTCGACGTC
GTAAAGTGCATTCTCATTGCCTCACCAGCTTTTGTAAAAGACGCATTCTTTGATTTTATG
ATTCAAACAGCGACAAGAACTGACCAAAAAGTCATTCTCGATAACAAGAGTAAATTTATG
TTAGTGCATGCATCATCTGGATTTAAGCATTCTCTCAAAGAGGTTCTACAAGATCCAGCA
GTGCTGGCTAAAATGAGCGATACTAAAGCAGCTGGCGAAGTGAAACGACTGGAAGCATTT
TACACAATGTTACAGTGCGATCCAAATCGAGCGTTTTATGGTAAAAAACATGTACAGAAG
GCGATTGACGCACAGGCTGTTGAAACACTTTTAATCTCAGATAATTTGTTTCGAAATCAG
GATTTAATTCAGCGTAAAGAATATGTTAAAATGCACGATGATGTACTCGATTCTGGTGGT
GATGTAAAAATATTCTCGAGCATGCACGTGTCTGGTGAACAACTAGCGCAACTGACAGGC
ATTGCCGCAATTTTGAGATTTCCTATGCCAGAACTAGAAGACGACGATTCTGAAGAAGAT
GAAAATTCTGATGCAGATTAAGTTTTGTAAATAACCGCTTAGAAAAAATAATGAACGATT
ATCATTCAAGTCATGTGTTCTAAAATATTATAACTTTTTTATTATGACAAATATAAAAAG
GAGGAAATTAACAATATTTCAGCTTCATGTTTTTATACGATATTTGCATAAAACAATTCA
AATAATTACGCAAGCTAATGATGATAAACGAAATTTAACTTTGTGAATTATGATTGCAAT
AAAAAAATATGAAAATTAAACTTATCAAAAAA
>g4944.t2 Gene=g4944 Length=386
MKLIFKNIDRGSGSIKMQPEEAEDMWHAYNLISIGDLITASTIRKVQNESSTGSSTSNRV
RTTLTLKIENIDYDTQACMLRLKGRNVVENDFVKMGAYHTIDLELNRPFTLTKPEWDSIA
LERVDMACDVTQNADVAAVIMQEGIAHICLITSNMTIVRSKIDMAIPRKRKNNSSQHDKG
LTKFYEAVMEGIKRHVNFDVVKCILIASPAFVKDAFFDFMIQTATRTDQKVILDNKSKFM
LVHASSGFKHSLKEVLQDPAVLAKMSDTKAAGEVKRLEAFYTMLQCDPNRAFYGKKHVQK
AIDAQAVETLLISDNLFRNQDLIQRKEYVKMHDDVLDSGGDVKIFSSMHVSGEQLAQLTG
IAAILRFPMPELEDDDSEEDENSDAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4944.t2 | Gene3D | G3DSA:2.30.30.870 | - | 1 | 131 | 0 |
| 11 | g4944.t2 | Gene3D | G3DSA:3.30.420.60 | - | 135 | 266 | 0 |
| 10 | g4944.t2 | Gene3D | G3DSA:3.30.1330.30 | - | 267 | 384 | 0 |
| 4 | g4944.t2 | PANTHER | PTHR10853 | PELOTA | 1 | 382 | 0 |
| 5 | g4944.t2 | PANTHER | PTHR10853:SF0 | PROTEIN PELOTA HOMOLOG | 1 | 382 | 0 |
| 3 | g4944.t2 | Pfam | PF03463 | eRF1 domain 1 | 1 | 128 | 0 |
| 2 | g4944.t2 | Pfam | PF03464 | eRF1 domain 2 | 135 | 265 | 0 |
| 1 | g4944.t2 | Pfam | PF03465 | eRF1 domain 3 | 271 | 369 | 0 |
| 9 | g4944.t2 | SMART | SM01194 | eRF1_1_2 | 1 | 129 | 0 |
| 6 | g4944.t2 | SUPERFAMILY | SSF159065 | Dom34/Pelota N-terminal domain-like | 1 | 129 | 0 |
| 7 | g4944.t2 | SUPERFAMILY | SSF53137 | Translational machinery components | 131 | 270 | 0 |
| 8 | g4944.t2 | SUPERFAMILY | SSF55315 | L30e-like | 264 | 369 | 0 |
| 13 | g4944.t2 | TIGRFAM | TIGR00111 | pelota: mRNA surveillance protein pelota | 1 | 369 | 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 transcript has been annotated with K06965 (protein pelota)
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.
