General information for g618.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein cabeza.
Parent gene
- The parent gene g618 is located on chr_3: 4532800..4533851 (- 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 | g618 | g618.t12 | TTS | g618.t12 | 4531187 | 4531187 |
| chr_3 | g618 | g618.t12 | isoform | g618.t12 | 4531392 | 4533851 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon1 | 4531392 | 4531453 |
| chr_3 | g618 | g618.t12 | cds | g618.t12.CDS1 | 4531392 | 4531453 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon2 | 4531572 | 4531898 |
| chr_3 | g618 | g618.t12 | cds | g618.t12.CDS2 | 4531572 | 4531898 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon3 | 4531981 | 4532214 |
| chr_3 | g618 | g618.t12 | cds | g618.t12.CDS3 | 4531981 | 4532214 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon4 | 4532277 | 4532396 |
| chr_3 | g618 | g618.t12 | cds | g618.t12.CDS4 | 4532277 | 4532396 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon5 | 4533552 | 4533612 |
| chr_3 | g618 | g618.t12 | cds | g618.t12.CDS5 | 4533552 | 4533600 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon6 | 4533688 | 4533759 |
| chr_3 | g618 | g618.t12 | exon | g618.t12.exon7 | 4533842 | 4533851 |
| chr_3 | g618 | g618.t12 | TSS | g618.t12 | 4534008 | 4534008 |
Sequences
>g618.t12 Gene=g618 Length=886
ATGGCAAATCAGGATTATAACAATTATCAAAGCTACGGTGGTGGCCAACAAGACTATGGA
AGTGGAAATAATTATGGTGGAGATTACCAAGGAAATGGAAACAATTATCGCGGTGGCAAT
TTCAACAAAGGAGGAAATTTTGGGCGGTAGTGGTGGCGATATGGTCGTTCAAGATGACAC
AATTTTCGTAAGTGGAATGGATCCTCAAATTACAGAATCAGAGATCAATAATCACTTTGG
AAGTATTGGTATTATCAAGAAAGACAAACGTACCAATAAGCCAAAAATTTGGATCTACAA
AGATAAAGCAACTGGTGAAGGCAAAGGTGAATGCACAATTACTTATGACGATCCTTGTAC
TGCATCAAGTGCAATAGAATGGTTCGATGGAAAGGAATTCAATGGTTATTCTATCAAAGT
TCAATTGGCTCAACGAAACAACAGTTGGCAAAAAGGTGGACCAAAGAAATTTGGTGGTCA
AGGCGGTGAAAGAGGAGGTCGAGGTGGATTTGGAGGAAGTGACAGAAATTTTTCACGACA
AAATGACGATCGAGGTCCGCGAGGTGGAGGAAGTGGTGGAAACTCAGGTGGACAACATCG
AGAAGGAGATTGGATTTGTTCAGAATGCTCTAATAAGAATTTTGCATGGCGAAATGAATG
TAACCGATGTAAGGAACCAAAAGGTGACAATGCTGGAAGTGCACCAAGTGGTGGCGGTGG
AAACAGAGGCTATGGCTCAGGTGATCGAGGTGGTCCACGAAATTTTGGAAATAGAGATGG
AGGAAATGGTGGCAACCGTAATTTTAATCGCGGCGGAATGAAAGGTGGCGATCGTCAATC
ATCAGGAGGAGGTGGTGGTGGTTTTAACAGACAAAGACCATATTAA
>g618.t12 Gene=g618 Length=263
METIIAVAISTKEEILGGSGGDMVVQDDTIFVSGMDPQITESEINNHFGSIGIIKKDKRT
NKPKIWIYKDKATGEGKGECTITYDDPCTASSAIEWFDGKEFNGYSIKVQLAQRNNSWQK
GGPKKFGGQGGERGGRGGFGGSDRNFSRQNDDRGPRGGGSGGNSGGQHREGDWICSECSN
KNFAWRNECNRCKEPKGDNAGSAPSGGGGNRGYGSGDRGGPRNFGNRDGGNGGNRNFNRG
GMKGGDRQSSGGGGGGFNRQRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g618.t12 | CDD | cd12534 | RRM_SARFH | 30 | 112 | 1.17612E-48 |
| 7 | g618.t12 | Gene3D | G3DSA:3.30.70.330 | - | 27 | 112 | 1.4E-21 |
| 6 | g618.t12 | Gene3D | G3DSA:4.10.1060.10 | Znf265 | 160 | 199 | 4.4E-11 |
| 13 | g618.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 169 | - |
| 12 | g618.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 196 | 263 | - |
| 3 | g618.t12 | PANTHER | PTHR23238 | RNA BINDING PROTEIN | 26 | 256 | 1.8E-62 |
| 2 | g618.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 30 | 108 | 3.3E-8 |
| 1 | g618.t12 | Pfam | PF00641 | Zn-finger in Ran binding protein and others | 169 | 197 | 3.6E-11 |
| 9 | g618.t12 | ProSitePatterns | PS01358 | Zinc finger RanBP2-type signature. | 173 | 192 | - |
| 15 | g618.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 28 | 114 | 12.953 |
| 14 | g618.t12 | ProSiteProfiles | PS50199 | Zinc finger RanBP2 type profile. | 169 | 198 | 10.557 |
| 11 | g618.t12 | SMART | SM00360 | rrm1_1 | 29 | 110 | 1.3E-12 |
| 10 | g618.t12 | SMART | SM00547 | zf_4 | 171 | 195 | 4.8E-6 |
| 4 | g618.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 26 | 143 | 1.61E-21 |
| 5 | g618.t12 | SUPERFAMILY | SSF90209 | Ran binding protein zinc finger-like | 161 | 199 | 4.24E-11 |
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:0003723 | RNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K13098 (RNA-binding protein FUS)
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. There were no conditions that were differentially expressed