General information for g11507.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Maternal protein pumilio.
Parent gene
- The parent gene g11507 is located on chr_1: 16701616..16702486 (+ 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 | g11507 | g11507.t8 | isoform | g11507.t8 | 16701616 | 16702486 |
| chr_1 | g11507 | g11507.t8 | exon | g11507.t8.exon1 | 16701616 | 16701876 |
| chr_1 | g11507 | g11507.t8 | exon | g11507.t8.exon2 | 16701952 | 16702120 |
| chr_1 | g11507 | g11507.t8 | cds | g11507.t8.CDS1 | 16702086 | 16702120 |
| chr_1 | g11507 | g11507.t8 | exon | g11507.t8.exon3 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t8 | cds | g11507.t8.CDS2 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t8 | TTS | g11507.t8 | 16702556 | 16702556 |
| chr_1 | g11507 | g11507.t8 | TSS | g11507.t8 | NA | NA |
Sequences
>g11507.t8 Gene=g11507 Length=737
GTGTAAAAGATCAAAACGGAAATCATGTCGTTCAGAAATGTATTGAGTGCGTAGATTCAA
CTGCATTACAATTTATTATAAATGCATTCAACGGACAAATTTTCACTTTAAGTACTCATC
CATATGGATGCAGAGTTATTCAAAGAATTTTGGAGCATTGTTCACCCGAACAAACAGCAC
CAATTTTACAGGAATTACATTTGAACACTGAAAAGCTTATTCAGGATCAATATGGAAATT
ATGTCATTCAGCATGTACTAGAACACGGTAAAGCTGAAGATAAATCTGCAATCATTAAAG
CAGTTCTTGGAAAAGTATTGACGCTCTCACAGCATAAATTTGCATCAAATGTTGTTGAAA
AATGTGTTACGCATGCTACAAGAGCTGAACGTAACATGTTAATTGATGAAGTTTGCATGT
TCAATGATACTGGACTTCAAGTGATGATGAAGGATCAATATGCCAATTACGTCGTTCAAA
AAATGATTGATGTATCAGAACCAACTCAAAGAAAGACGCTTTTGCACAAGATTCGACCAC
ACATGAATTCCTTACGCAAGTACACTTATGGCAAGCATATTATTGCAAAGTTGGAAAAAT
TCTCTTTAAAATCTGGTGTAGCTTCTGTAACAACTTCTTCTACAGCTACCACTAATCCTA
ACACGTCGTCTACAACAGCTACTGATACTGTTACTTCTTCGACATCATCGTCGTCTTTTG
GAGCAAACGGTTTATAA
>g11507.t8 Gene=g11507 Length=113
MLIDEVCMFNDTGLQVMMKDQYANYVVQKMIDVSEPTQRKTLLHKIRPHMNSLRKYTYGK
HIIAKLEKFSLKSGVASVTTSSTATTNPNTSSTTATDTVTSSTSSSSFGANGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11507.t8 | Gene3D | G3DSA:1.25.10.10 | - | 1 | 68 | 1.2E-22 |
| 6 | g11507.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 79 | 113 | - |
| 2 | g11507.t8 | PANTHER | PTHR12537:SF1 | PUMILIO HOMOLOG 1 | 1 | 79 | 2.0E-35 |
| 3 | g11507.t8 | PANTHER | PTHR12537 | RNA BINDING PROTEIN PUMILIO-RELATED | 1 | 79 | 2.0E-35 |
| 1 | g11507.t8 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 17 | 46 | 9.7E-8 |
| 10 | g11507.t8 | ProSiteProfiles | PS50303 | Pumilio homology domain (PUM-HD) profile. | 1 | 70 | 22.896 |
| 8 | g11507.t8 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 8 | 44 | 9.154 |
| 9 | g11507.t8 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 45 | 80 | 4.558 |
| 5 | g11507.t8 | SMART | SM00025 | pum_5 | 9 | 44 | 1.7E-6 |
| 4 | g11507.t8 | SUPERFAMILY | SSF48371 | ARM repeat | 2 | 67 | 1.67E-14 |
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:0003723 | RNA binding | MF |
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.
