General information for g568.t6
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.t6 | isoform | g568.t6 | 4173512 | 4175310 |
| chr_3 | g568 | g568.t6 | exon | g568.t6.exon1 | 4173512 | 4173667 |
| chr_3 | g568 | g568.t6 | cds | g568.t6.CDS1 | 4173612 | 4173667 |
| chr_3 | g568 | g568.t6 | exon | g568.t6.exon2 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t6 | cds | g568.t6.CDS2 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t6 | exon | g568.t6.exon3 | 4174432 | 4174763 |
| chr_3 | g568 | g568.t6 | cds | g568.t6.CDS3 | 4174432 | 4174763 |
| chr_3 | g568 | g568.t6 | exon | g568.t6.exon4 | 4174824 | 4175310 |
| chr_3 | g568 | g568.t6 | cds | g568.t6.CDS4 | 4174824 | 4174913 |
| chr_3 | g568 | g568.t6 | TSS | g568.t6 | NA | NA |
| chr_3 | g568 | g568.t6 | TTS | g568.t6 | NA | NA |
Sequences
>g568.t6 Gene=g568 Length=1622
AGCATGGGAAAGTAGAGAAAGAAAAAAAGCTAAAGAATATGAAAAACTAAGGGAGAAAGA
AATTAAGCGTGAAGAAAAACGTGAAAGGGAAGCCAAAATTATGAAAGAATTTTTAGAAGA
TTATGACGATGAGCGTGATGATCCTAAATTTTATAAAGGGAAAGCTTATAAAACACTCAT
GGCAGAACGATTGGCAGAAGCTGATGCAGACTTAAAGGATCGTGAAGAAGAACGCGAAGA
GCTAGAAAAACTGAAAGAAGAAATTTTCAGTGGTAAATATGACAATCCGACACAAGAATT
TGAACGACAAAAACAAGAAATGGAAGAACGATATAAACCCAAGATTTTAATTGACGTAAA
CATGGATGAAGATGACCAACAAGAATATCATAGAGATAAGACTCGAGAACAAGACAGGGC
GAAAGCTAGAGAACGAAGAATAACACAAAAAGATAGATATGTTAAGGACAAATCTTCACG
TGAATTTTCAAGTCTTGATGCCGAACCAATTGAGTCTGATTCAAGTGGAGGTCACAATTT
TTCACCATCAAATAATCGAGGTGGATCAGAATCAAGAGACGGCATGGACGATGAGATGTC
GAGAAACTCTTTGCTTTCCAATTCAAATACACCAACAACACCCAATAGTCCGTCTGGTAA
TCAAAATTCAGCAACAGGAATTGGAATGGGCTTTAGTTTGAGTTTAAATAAAAAGAGAAA
AATTGATCCTAAGAGTGCATTTGCATTGGATGATGATGGTGAAGAAGTAAATGGTCCACA
GAAAAAGAAATTAGTACCTCTTGATTATGAAGATGGCTCGTCTAATGCAAAGAAGACTAA
ACGCGATGGTGAAGCTCAAAAGAAAACAGAAGCTGATATTGCACGCTCACAGGAAGAAAA
ACGAAAACTGCACAAACAAATTATCAATAAGATTCCAATTGATAAAGAAGATCTCTTCAA
TCATCCACTCGATCGTACAGAAATTGATGGTACAATAAAGAAGAAAGTTCAGTCATGGAT
CAATAAGAAAATTATTGAATATATTGGTGAGCCAGAACCTACACTAGTTGATTTTATTTG
TTCTAAGTTACTAGCGGGAAGTACACCACAGTCCATATTGGATGATGTAAAAATGATTCT
CGATGAAGAAGCTGATATATTTGTTGTAAAAATGTGGCGACTGATAATCTTTGAAGTGGA
AGCAAAAAAGCTTGGAATTAAATAATCAGCTGCTGACTGTGTAAGCATCAAATATAACAA
TGAGACTAAATTCATTGAACATATAAAATAAATAAAAATCTTCTTTTCATATTGATTTTT
GCACTACTACATTAAATTGAAAAAATAGATTAAAAGCCTCGTAATGATTGAATCACGGGA
TATGAGAGTCCGTTGTTATCAATTTTCATTTTGGGTAAATATCTATTAAAATCATGCAAA
ATTAAAAAGATATATAAAACATTGGAATATTAGAAAAACTTTAAAAAATGATAAATATAA
CTATTATGAAAATAATGATACACAACACTTTAAATTTAAGCATTAATTGATTATTCCTTC
ATCTTAATCTTAATCATTATTGAAGTGAAGATAAAATTTGAGAAAATAAAGATAAATTTT
GA
>g568.t6 Gene=g568 Length=374
MKEFLEDYDDERDDPKFYKGKAYKTLMAERLAEADADLKDREEEREELEKLKEEIFSGKY
DNPTQEFERQKQEMEERYKPKILIDVNMDEDDQQEYHRDKTREQDRAKARERRITQKDRY
VKDKSSREFSSLDAEPIESDSSGGHNFSPSNNRGGSESRDGMDDEMSRNSLLSNSNTPTT
PNSPSGNQNSATGIGMGFSLSLNKKRKIDPKSAFALDDDGEEVNGPQKKKLVPLDYEDGS
SNAKKTKRDGEAQKKTEADIARSQEEKRKLHKQIINKIPIDKEDLFNHPLDRTEIDGTIK
KKVQSWINKKIIEYIGEPEPTLVDFICSKLLAGSTPQSILDDVKMILDEEADIFVVKMWR
LIIFEVEAKKLGIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g568.t6 | Coils | Coil | Coil | 31 | 54 | - |
| 6 | g568.t6 | Coils | Coil | Coil | 253 | 273 | - |
| 4 | g568.t6 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 259 | 374 | 3.9E-39 |
| 9 | g568.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 198 | - |
| 11 | g568.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 134 | - |
| 8 | g568.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 135 | 156 | - |
| 12 | g568.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 167 | 197 | - |
| 10 | g568.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 213 | 265 | - |
| 2 | g568.t6 | PANTHER | PTHR18806 | RBM25 PROTEIN | 1 | 373 | 2.4E-93 |
| 1 | g568.t6 | Pfam | PF01480 | PWI domain | 302 | 366 | 3.3E-11 |
| 13 | g568.t6 | ProSiteProfiles | PS51025 | PWI domain profile. | 283 | 374 | 32.58 |
| 7 | g568.t6 | SMART | SM00311 | pwi_2 | 295 | 368 | 2.7E-23 |
| 3 | g568.t6 | SUPERFAMILY | SSF101233 | PWI domain | 284 | 365 | 1.11E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g568/g568.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g568.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006397 | mRNA processing | BP |
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.
