General information for g568.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein 25.
Parent gene
- The parent gene g568 is located on chr_3: 4173512..4175310 (+ 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 | g568 | g568.t4 | isoform | g568.t4 | 4173062 | 4174762 |
| chr_3 | g568 | g568.t4 | exon | g568.t4.exon1 | 4173062 | 4173447 |
| chr_3 | g568 | g568.t4 | cds | g568.t4.CDS1 | 4173293 | 4173447 |
| chr_3 | g568 | g568.t4 | exon | g568.t4.exon2 | 4173512 | 4173667 |
| chr_3 | g568 | g568.t4 | cds | g568.t4.CDS2 | 4173512 | 4173667 |
| chr_3 | g568 | g568.t4 | exon | g568.t4.exon3 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t4 | cds | g568.t4.CDS3 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t4 | exon | g568.t4.exon4 | 4174432 | 4174762 |
| chr_3 | g568 | g568.t4 | cds | g568.t4.CDS4 | 4174432 | 4174760 |
| chr_3 | g568 | g568.t4 | TSS | g568.t4 | NA | NA |
| chr_3 | g568 | g568.t4 | TTS | g568.t4 | NA | NA |
Sequences
>g568.t4 Gene=g568 Length=1520
GATAAAAAGAAGCGTGAAAATTTAGAAAAAGAAAGAAGTGAAAGAAATGAAAAGAGACAT
ACACCTTCACCAGAACGAAAAAGTTCTTCAAGACGTCGTTCTAGGTCTAGAGATAGAGAC
AGAGAAGCCCAACGTGAGCGTGACAGAGAACAACGTGAACGTGAGAGGGAGAGGGAAAGA
GAACGACGCGAAATTGATCGTCGACGTGAACAAGAACTAAGAGAAAAAGAAATGCGTGAG
CGTGAAAGATTTCGAGAGGAACCAAAGCAGATGAAAAATGCAAAAGAAATTCAACGTGAG
AAAGAAATTGCTGAAGAAGAATATGAACGTCGTAGAGCACAGAAAAAAGCTCGTGAAAAA
CATGAAGATTATTTAGCAAGATTAGAAGCATGGGAAAGTAGAGAAAGAAAAAAAGCTAAA
GAATATGAAAAACTAAGGGAGAAAGAAATTAAGCGTGAAGAAAAACGTGAAAGGGAAGCC
AAAATTATGAAAGAATTTTTAGAAGATTATGACGATGAGCGTGATGATCCTAAATTTTAT
AAAGGGAAAGCTTATAAAACACTCATGGCAGAACGATTGGCAGAAGCTGATGCAGACTTA
AAGGATCGTGAAGAAGAACGCGAAGAGCTAGAAAAACTGAAAGAAGAAATTTTCAGTGGT
AAATATGACAATCCGACACAAGAATTTGAACGACAAAAACAAGAAATGGAAGAACGATAT
AAACCCAAGATTTTAATTGACGTAAACATGGATGAAGATGACCAACAAGAATATCATAGA
GATAAGACTCGAGAACAAGACAGGGCGAAAGCTAGAGAACGAAGAATAACACAAAAAGAT
AGATATGTTAAGGACAAATCTTCACGTGAATTTTCAAGTCTTGATGCCGAACCAATTGAG
TCTGATTCAAGTGGAGGTCACAATTTTTCACCATCAAATAATCGAGGTGGATCAGAATCA
AGAGACGGCATGGACGATGAGATGTCGAGAAACTCTTTGCTTTCCAATTCAAATACACCA
ACAACACCCAATAGTCCGTCTGGTAATCAAAATTCAGCAACAGGAATTGGAATGGGCTTT
AGTTTGAGTTTAAATAAAAAGAGAAAAATTGATCCTAAGAGTGCATTTGCATTGGATGAT
GATGGTGAAGAAGTAAATGGTCCACAGAAAAAGAAATTAGTACCTCTTGATTATGAAGAT
GGCTCGTCTAATGCAAAGAAGACTAAACGCGATGGTGAAGCTCAAAAGAAAACAGAAGCT
GATATTGCACGCTCACAGGAAGAAAAACGAAAACTGCACAAACAAATTATCAATAAGATT
CCAATTGATAAAGAAGATCTCTTCAATCATCCACTCGATCGTACAGAAATTGATGGTACA
ATAAAGAAGAAAGTTCAGTCATGGATCAATAAGAAAATTATTGAATATATTGGTGAGCCA
GAACCTACACTAGTTGATTTTATTTGTTCTAAGTTACTAGCGGGAAGTACACCACAGTCC
ATATTGGATGATGTAAAAAT
>g568.t4 Gene=g568 Length=429
MRERERFREEPKQMKNAKEIQREKEIAEEEYERRRAQKKAREKHEDYLARLEAWESRERK
KAKEYEKLREKEIKREEKREREAKIMKEFLEDYDDERDDPKFYKGKAYKTLMAERLAEAD
ADLKDREEEREELEKLKEEIFSGKYDNPTQEFERQKQEMEERYKPKILIDVNMDEDDQQE
YHRDKTREQDRAKARERRITQKDRYVKDKSSREFSSLDAEPIESDSSGGHNFSPSNNRGG
SESRDGMDDEMSRNSLLSNSNTPTTPNSPSGNQNSATGIGMGFSLSLNKKRKIDPKSAFA
LDDDGEEVNGPQKKKLVPLDYEDGSSNAKKTKRDGEAQKKTEADIARSQEEKRKLHKQII
NKIPIDKEDLFNHPLDRTEIDGTIKKKVQSWINKKIIEYIGEPEPTLVDFICSKLLAGST
PQSILDDVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g568.t4 | Coils | Coil | Coil | 14 | 88 | - |
| 11 | g568.t4 | Coils | Coil | Coil | 116 | 139 | - |
| 10 | g568.t4 | Coils | Coil | Coil | 338 | 358 | - |
| 8 | g568.t4 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 344 | 429 | 1.2E-22 |
| 5 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 42 | - |
| 3 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 219 | - |
| 4 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 283 | - |
| 7 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 220 | 241 | - |
| 2 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 282 | - |
| 6 | g568.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 298 | 353 | - |
| 1 | g568.t4 | PANTHER | PTHR18806 | RBM25 PROTEIN | 2 | 429 | 1.7E-93 |
| 12 | g568.t4 | ProSiteProfiles | PS51025 | PWI domain profile. | 368 | 429 | 19.165 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g568/g568.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g568.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006397 | mRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K12822 (RNA-binding protein 25)
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.
