General information for g1138.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Poly(U)-binding-splicing factor half pint.
Parent gene
- The parent gene g1138 is located on chr_3: 8380940..8381516 (+ 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_3 | g1138 | g1138.t6 | isoform | g1138.t6 | 8380940 | 8381516 |
| chr_3 | g1138 | g1138.t6 | exon | g1138.t6.exon1 | 8380940 | 8381346 |
| chr_3 | g1138 | g1138.t6 | cds | g1138.t6.CDS1 | 8381085 | 8381346 |
| chr_3 | g1138 | g1138.t6 | exon | g1138.t6.exon2 | 8381407 | 8381516 |
| chr_3 | g1138 | g1138.t6 | cds | g1138.t6.CDS2 | 8381407 | 8381516 |
| chr_3 | g1138 | g1138.t6 | TTS | g1138.t6 | 8381717 | 8381717 |
| chr_3 | g1138 | g1138.t6 | TSS | g1138.t6 | NA | NA |
Sequences
>g1138.t6 Gene=g1138 Length=517
ACCAATTGGCGTCTCTACAAATTTACCTTCATTGATATCAAATGAAACACAACAGAATGC
AGAAGAATTGGTAAAACAAAAACAAGAAGAATTACAAAAGAAATTATTAGAAGAGGGTGA
ACCAACTTTACAACAACAAGAATCAATGTCCATCAAAGGTCAAAATGCAAGACATTTAGT
CATGCAAAGACTTATGAGACCACGTGAAAGTAAAGTTGTAATTTTAAGAAATATGGTTGG
ACCTGAAGATGTTGATGAGACACTTCAAGAAGAAATTCAAGATGAATGCAGTAAATATGG
TGTTGTAGAGAAAGTTATTATTTATAAAGAGAAACAAACTGACAATGATGATGACGATTA
TGGTGATGTTATTGTAAAAATTTTCGTAGAATTTTCGATGTCATCTGAAGCTGACAAGGC
AAGTTCTGGTTTAAATGGTCGATTTTTTGGAGGACGATTGGTTAAAGCTGAGAGCTACGA
CCAAGCACTTTTTGACCACAGTGACTTTTCTGGTTGA
>g1138.t6 Gene=g1138 Length=123
MSIKGQNARHLVMQRLMRPRESKVVILRNMVGPEDVDETLQEEIQDECSKYGVVEKVIIY
KEKQTDNDDDDYGDVIVKIFVEFSMSSEADKASSGLNGRFFGGRLVKAESYDQALFDHSD
FSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1138.t6 | Gene3D | G3DSA:3.30.70.330 | - | 22 | 112 | 0.000000 |
| 2 | g1138.t6 | PANTHER | PTHR47330 | POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED | 1 | 123 | 0.000000 |
| 3 | g1138.t6 | PANTHER | PTHR47330:SF1 | POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED | 1 | 123 | 0.000000 |
| 1 | g1138.t6 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 39 | 106 | 0.000019 |
| 7 | g1138.t6 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 23 | 113 | 9.729000 |
| 5 | g1138.t6 | SMART | SM00361 | rrm2_1 | 24 | 109 | 0.000000 |
| 4 | g1138.t6 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 27 | 112 | 0.000000 |
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:0003676 | nucleic acid 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.
