General information for g8808.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor SPF27.
Parent gene
- The parent gene g8808 is located on chr_2: 33264464..33265282 (- 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 | g8808 | g8808.t1 | TTS | g8808.t1 | 33264446 | 33264446 |
| chr_2 | g8808 | g8808.t1 | isoform | g8808.t1 | 33264464 | 33265282 |
| chr_2 | g8808 | g8808.t1 | exon | g8808.t1.exon1 | 33264464 | 33265147 |
| chr_2 | g8808 | g8808.t1 | cds | g8808.t1.CDS1 | 33264464 | 33265147 |
| chr_2 | g8808 | g8808.t1 | exon | g8808.t1.exon2 | 33265208 | 33265282 |
| chr_2 | g8808 | g8808.t1 | cds | g8808.t1.CDS2 | 33265208 | 33265282 |
| chr_2 | g8808 | g8808.t1 | TSS | g8808.t1 | 33265369 | 33265369 |
Sequences
>g8808.t1 Gene=g8808 Length=759
ATGACTTCAGAAATACTTGTTGATGCATTACCATACTTTGATGTTGGATTTGATGAGCCG
GGAGTTCGAGAAATGGCACTTGCCATGGTAGATGAAGAATGCAGAAGATATAAACCTTCA
AAAAATTATCTCGAACATATGTCATTAGATACAACAACATCATTTGAGACTGAACTTATG
AAGAATGAATTTCAAAGAATTGAAAGCGGAGCAAGACTTGATTCAATGAACACTAAACGA
TATGAATTGCCAGCTCCTCCTTCGGGAAAACTGAGTGAAATTCAAGCATGGCAGGAAAGC
GTTGATAATTCATTTGCGCAATTAGAACATCAAGCGATTCGTTATTTAAATCTCGAGCTT
CTACAAAAATATGGATGTGAAAGTTGGAAAGCTGCACTTGAAGTCCTCGTTGGTCTCAAT
GCGAAAGCACAAAAAGAATTACAAGAGCTTAAAAAAGAAATTCAAGATGTCAATTGGAGA
CGCAAAACGAAGCAGTTGCAGACAGGAGATAGATTAAATCAACTTAATAACACTTGGGTA
CAGCTTGTTTCTTGCAATTTTGAGCTTGAGTCTGCTATAAAGCAGTTAGAAATTCAAATA
GCATTACATCAAAATGGTCAACAAGAGCAATCAAATGGTCATGACAAGAATGAAAATGAA
GAGGAAGAAAAGGTTGAAAATCACGAAAATGGAACCATTGATACAGAAAATAATCAAAAT
AATGATAATCATGATGAGGACGTTGAAATGAAGGAATAA
>g8808.t1 Gene=g8808 Length=252
MTSEILVDALPYFDVGFDEPGVREMALAMVDEECRRYKPSKNYLEHMSLDTTTSFETELM
KNEFQRIESGARLDSMNTKRYELPAPPSGKLSEIQAWQESVDNSFAQLEHQAIRYLNLEL
LQKYGCESWKAALEVLVGLNAKAQKELQELKKEIQDVNWRRKTKQLQTGDRLNQLNNTWV
QLVSCNFELESAIKQLEIQIALHQNGQQEQSNGHDKNENEEEEKVENHENGTIDTENNQN
NDNHDEDVEMKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8808.t1 | Coils | Coil | Coil | 133 | 167 | - |
| 4 | g8808.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 205 | 252 | - |
| 5 | g8808.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 213 | 231 | - |
| 2 | g8808.t1 | PANTHER | PTHR13296:SF4 | PRE-MRNA-SPLICING FACTOR SPF27 | 3 | 208 | 9.4E-69 |
| 3 | g8808.t1 | PANTHER | PTHR13296 | BCAS2 PROTEIN | 3 | 208 | 9.4E-69 |
| 1 | g8808.t1 | Pfam | PF05700 | Breast carcinoma amplified sequence 2 (BCAS2) | 6 | 209 | 2.0E-65 |
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:0006397 | mRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K12861 (pre-mRNA-splicing factor SPF27)
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.
