General information for g568.t1
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.t1 | TSS | g568.t1 | 4171916 | 4171916 |
| chr_3 | g568 | g568.t1 | isoform | g568.t1 | 4172173 | 4174913 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon1 | 4172173 | 4172229 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS1 | 4172173 | 4172229 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon2 | 4172294 | 4172420 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS2 | 4172294 | 4172420 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon3 | 4172485 | 4172593 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS3 | 4172485 | 4172593 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon4 | 4172665 | 4173447 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS4 | 4172665 | 4173447 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon5 | 4173512 | 4173667 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS5 | 4173512 | 4173667 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon6 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS6 | 4173726 | 4174372 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon7 | 4174432 | 4174763 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS7 | 4174432 | 4174763 |
| chr_3 | g568 | g568.t1 | exon | g568.t1.exon8 | 4174824 | 4174913 |
| chr_3 | g568 | g568.t1 | cds | g568.t1.CDS8 | 4174824 | 4174913 |
| chr_3 | g568 | g568.t1 | TTS | g568.t1 | NA | NA |
Sequences
>g568.t1 Gene=g568 Length=2301
ATGTTTAACAATAATCAAGCCCGACATCCGCCTCCTCATCAAATGTATGCGCCACCACCG
CCTAGAGAAAATTATGGCAAAACTATAGGCTCAGGGCCTCAATTTTATACTAAACCACCT
ACAAATATTCCATCTAATCAAACAATTGAATTTGATGAAGGTCCGAAAATTACTGTCTTT
GTTGGTAACATTAGTGATAAGATTCCAGATGCAATGATTAAAAAATTAATAGCAGCTTGT
GGACCAGTAGCGAATTGGAAACGAGTATCAACTTTCGGTTTCTGTGAATATGATGGACCA
AAATCAGGAGCTCGAGCTGTTAGACTATTGCATGGATATGAAGTTGATGGCAAAAAATTA
GTAGCAAAAGTAGATGCCAAAAATCAAGCTTTACTTGACACAGCAAAAGATGAAGAAAAT
AAAAAGTCGGATGCAAATAACACTAGAAATTCTGATGCAGCAAATGAAAAGAAGAATGAC
GAGATTGCACTTGAACGATTGCATCAAATTGTAGAAGAATATAAAGATGAATTAAAAACA
GCAAATTCAGCTGAAAATCAACAACCGCATCCACGAAGTAAGCAAACTGTGCCATCAATT
GAAATTGAGGAAGGGAAACGAGATTTAATAAATAAAGAAATTGGAAGATTTCGTAAGATT
GCTGAAGAAGAAGAGGCCAAGAAAGAAAAAGATAAAAAGAAGCGTGAAAATTTAGAAAAA
GAAAGAAGTGAAAGAAATGAAAAGAGACATACACCTTCACCAGAACGAAAAAGTTCTTCA
AGACGTCGTTCTAGGTCTAGAGATAGAGACAGAGAAGCCCAACGTGAGCGTGACAGAGAA
CAACGTGAACGTGAGAGGGAGAGGGAAAGAGAACGACGCGAAATTGATCGTCGACGTGAA
CAAGAACTAAGAGAAAAAGAAATGCGTGAGCGTGAAAGATTTCGAGAGGAACCAAAGCAG
ATGAAAAATGCAAAAGAAATTCAACGTGAGAAAGAAATTGCTGAAGAAGAATATGAACGT
CGTAGAGCACAGAAAAAAGCTCGTGAAAAACATGAAGATTATTTAGCAAGATTAGAAGCA
TGGGAAAGTAGAGAAAGAAAAAAAGCTAAAGAATATGAAAAACTAAGGGAGAAAGAAATT
AAGCGTGAAGAAAAACGTGAAAGGGAAGCCAAAATTATGAAAGAATTTTTAGAAGATTAT
GACGATGAGCGTGATGATCCTAAATTTTATAAAGGGAAAGCTTATAAAACACTCATGGCA
GAACGATTGGCAGAAGCTGATGCAGACTTAAAGGATCGTGAAGAAGAACGCGAAGAGCTA
GAAAAACTGAAAGAAGAAATTTTCAGTGGTAAATATGACAATCCGACACAAGAATTTGAA
CGACAAAAACAAGAAATGGAAGAACGATATAAACCCAAGATTTTAATTGACGTAAACATG
GATGAAGATGACCAACAAGAATATCATAGAGATAAGACTCGAGAACAAGACAGGGCGAAA
GCTAGAGAACGAAGAATAACACAAAAAGATAGATATGTTAAGGACAAATCTTCACGTGAA
TTTTCAAGTCTTGATGCCGAACCAATTGAGTCTGATTCAAGTGGAGGTCACAATTTTTCA
CCATCAAATAATCGAGGTGGATCAGAATCAAGAGACGGCATGGACGATGAGATGTCGAGA
AACTCTTTGCTTTCCAATTCAAATACACCAACAACACCCAATAGTCCGTCTGGTAATCAA
AATTCAGCAACAGGAATTGGAATGGGCTTTAGTTTGAGTTTAAATAAAAAGAGAAAAATT
GATCCTAAGAGTGCATTTGCATTGGATGATGATGGTGAAGAAGTAAATGGTCCACAGAAA
AAGAAATTAGTACCTCTTGATTATGAAGATGGCTCGTCTAATGCAAAGAAGACTAAACGC
GATGGTGAAGCTCAAAAGAAAACAGAAGCTGATATTGCACGCTCACAGGAAGAAAAACGA
AAACTGCACAAACAAATTATCAATAAGATTCCAATTGATAAAGAAGATCTCTTCAATCAT
CCACTCGATCGTACAGAAATTGATGGTACAATAAAGAAGAAAGTTCAGTCATGGATCAAT
AAGAAAATTATTGAATATATTGGTGAGCCAGAACCTACACTAGTTGATTTTATTTGTTCT
AAGTTACTAGCGGGAAGTACACCACAGTCCATATTGGATGATGTAAAAATGATTCTCGAT
GAAGAAGCTGATATATTTGTTGTAAAAATGTGGCGACTGATAATCTTTGAAGTGGAAGCA
AAAAAGCTTGGAATTAAATAA
>g568.t1 Gene=g568 Length=766
MFNNNQARHPPPHQMYAPPPPRENYGKTIGSGPQFYTKPPTNIPSNQTIEFDEGPKITVF
VGNISDKIPDAMIKKLIAACGPVANWKRVSTFGFCEYDGPKSGARAVRLLHGYEVDGKKL
VAKVDAKNQALLDTAKDEENKKSDANNTRNSDAANEKKNDEIALERLHQIVEEYKDELKT
ANSAENQQPHPRSKQTVPSIEIEEGKRDLINKEIGRFRKIAEEEEAKKEKDKKKRENLEK
ERSERNEKRHTPSPERKSSSRRRSRSRDRDREAQRERDREQRERERERERERREIDRRRE
QELREKEMRERERFREEPKQMKNAKEIQREKEIAEEEYERRRAQKKAREKHEDYLARLEA
WESRERKKAKEYEKLREKEIKREEKREREAKIMKEFLEDYDDERDDPKFYKGKAYKTLMA
ERLAEADADLKDREEEREELEKLKEEIFSGKYDNPTQEFERQKQEMEERYKPKILIDVNM
DEDDQQEYHRDKTREQDRAKARERRITQKDRYVKDKSSREFSSLDAEPIESDSSGGHNFS
PSNNRGGSESRDGMDDEMSRNSLLSNSNTPTTPNSPSGNQNSATGIGMGFSLSLNKKRKI
DPKSAFALDDDGEEVNGPQKKKLVPLDYEDGSSNAKKTKRDGEAQKKTEADIARSQEEKR
KLHKQIINKIPIDKEDLFNHPLDRTEIDGTIKKKVQSWINKKIIEYIGEPEPTLVDFICS
KLLAGSTPQSILDDVKMILDEEADIFVVKMWRLIIFEVEAKKLGIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g568.t1 | CDD | cd12446 | RRM_RBM25 | 58 | 132 | 1.19786E-29 |
| 14 | g568.t1 | Coils | Coil | Coil | 121 | 148 | - |
| 11 | g568.t1 | Coils | Coil | Coil | 157 | 187 | - |
| 13 | g568.t1 | Coils | Coil | Coil | 219 | 248 | - |
| 8 | g568.t1 | Coils | Coil | Coil | 270 | 317 | - |
| 9 | g568.t1 | Coils | Coil | Coil | 321 | 395 | - |
| 10 | g568.t1 | Coils | Coil | Coil | 423 | 446 | - |
| 12 | g568.t1 | Coils | Coil | Coil | 645 | 665 | - |
| 6 | g568.t1 | Gene3D | G3DSA:3.30.70.330 | - | 51 | 152 | 1.1E-11 |
| 7 | g568.t1 | Gene3D | G3DSA:1.20.1390.10 | PWI domain | 651 | 766 | 1.3E-38 |
| 24 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 135 | 161 | - |
| 25 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 180 | 204 | - |
| 19 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 181 | 195 | - |
| 23 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 328 | - |
| 18 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 442 | 590 | - |
| 21 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 442 | 526 | - |
| 22 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 527 | 548 | - |
| 26 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 559 | 589 | - |
| 20 | g568.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 605 | 657 | - |
| 3 | g568.t1 | PANTHER | PTHR18806 | RBM25 PROTEIN | 8 | 765 | 4.7E-181 |
| 2 | g568.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 59 | 120 | 1.1E-5 |
| 1 | g568.t1 | Pfam | PF01480 | PWI domain | 694 | 758 | 9.3E-11 |
| 28 | g568.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 57 | 127 | 10.343 |
| 27 | g568.t1 | ProSiteProfiles | PS51025 | PWI domain profile. | 675 | 766 | 32.58 |
| 17 | g568.t1 | SMART | SM00360 | rrm1_1 | 58 | 123 | 6.3E-9 |
| 16 | g568.t1 | SMART | SM00311 | pwi_2 | 687 | 760 | 2.7E-23 |
| 4 | g568.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 23 | 123 | 3.33E-13 |
| 5 | g568.t1 | SUPERFAMILY | SSF101233 | PWI domain | 676 | 757 | 3.4E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g568/g568.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g568.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006397 | mRNA processing | BP |
| GO:0003676 | nucleic acid binding | MF |
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.
