General information for g618.t1
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.t1 | TTS | g618.t1 | 4531187 | 4531187 |
| chr_3 | g618 | g618.t1 | isoform | g618.t1 | 4531392 | 4533851 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon1 | 4531392 | 4531453 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS1 | 4531392 | 4531453 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon2 | 4531572 | 4531898 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS2 | 4531572 | 4531898 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon3 | 4531981 | 4532214 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS3 | 4531981 | 4532214 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon4 | 4532277 | 4532396 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS4 | 4532277 | 4532396 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon5 | 4532820 | 4532854 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS5 | 4532820 | 4532854 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon6 | 4533552 | 4533612 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS6 | 4533552 | 4533612 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon7 | 4533682 | 4533759 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS7 | 4533682 | 4533759 |
| chr_3 | g618 | g618.t1 | exon | g618.t1.exon8 | 4533842 | 4533851 |
| chr_3 | g618 | g618.t1 | cds | g618.t1.CDS8 | 4533842 | 4533851 |
| chr_3 | g618 | g618.t1 | TSS | g618.t1 | 4534008 | 4534008 |
Sequences
>g618.t1 Gene=g618 Length=927
ATGGCAAATCAGGATTATAACAATTATCAAAGCTACGGTGGTGGCCAACAAGACTATGGA
AGTGGAAATAATTATGGTGGAGGTAATGATTACCAAGGAAATGGAAACAATTATCGCGGT
GGCAATTTCAACAAAGGAGGAAATTTTGGCGGAAACAACAGAAGTGGTGGTTATAATAAC
AAAGGCGGTAGTGGTGGCGATATGGTCGTTCAAGATGACACAATTTTCGTAAGTGGAATG
GATCCTCAAATTACAGAATCAGAGATCAATAATCACTTTGGAAGTATTGGTATTATCAAG
AAAGACAAACGTACCAATAAGCCAAAAATTTGGATCTACAAAGATAAAGCAACTGGTGAA
GGCAAAGGTGAATGCACAATTACTTATGACGATCCTTGTACTGCATCAAGTGCAATAGAA
TGGTTCGATGGAAAGGAATTCAATGGTTATTCTATCAAAGTTCAATTGGCTCAACGAAAC
AACAGTTGGCAAAAAGGTGGACCAAAGAAATTTGGTGGTCAAGGCGGTGAAAGAGGAGGT
CGAGGTGGATTTGGAGGAAGTGACAGAAATTTTTCACGACAAAATGACGATCGAGGTCCG
CGAGGTGGAGGAAGTGGTGGAAACTCAGGTGGACAACATCGAGAAGGAGATTGGATTTGT
TCAGAATGCTCTAATAAGAATTTTGCATGGCGAAATGAATGTAACCGATGTAAGGAACCA
AAAGGTGACAATGCTGGAAGTGCACCAAGTGGTGGCGGTGGAAACAGAGGCTATGGCTCA
GGTGATCGAGGTGGTCCACGAAATTTTGGAAATAGAGATGGAGGAAATGGTGGCAACCGT
AATTTTAATCGCGGCGGAATGAAAGGTGGCGATCGTCAATCATCAGGAGGAGGTGGTGGT
GGTTTTAACAGACAAAGACCATATTAA
>g618.t1 Gene=g618 Length=308
MANQDYNNYQSYGGGQQDYGSGNNYGGGNDYQGNGNNYRGGNFNKGGNFGGNNRSGGYNN
KGGSGGDMVVQDDTIFVSGMDPQITESEINNHFGSIGIIKKDKRTNKPKIWIYKDKATGE
GKGECTITYDDPCTASSAIEWFDGKEFNGYSIKVQLAQRNNSWQKGGPKKFGGQGGERGG
RGGFGGSDRNFSRQNDDRGPRGGGSGGNSGGQHREGDWICSECSNKNFAWRNECNRCKEP
KGDNAGSAPSGGGGNRGYGSGDRGGPRNFGNRDGGNGGNRNFNRGGMKGGDRQSSGGGGG
GFNRQRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g618.t1 | CDD | cd12534 | RRM_SARFH | 75 | 157 | 1.34512E-48 |
| 7 | g618.t1 | Gene3D | G3DSA:3.30.70.330 | - | 72 | 157 | 2.0E-21 |
| 6 | g618.t1 | Gene3D | G3DSA:4.10.1060.10 | Znf265 | 205 | 244 | 5.5E-11 |
| 12 | g618.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 161 | 214 | - |
| 13 | g618.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 241 | 308 | - |
| 3 | g618.t1 | PANTHER | PTHR23238 | RNA BINDING PROTEIN | 9 | 301 | 6.9E-54 |
| 2 | g618.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 75 | 153 | 4.5E-8 |
| 1 | g618.t1 | Pfam | PF00641 | Zn-finger in Ran binding protein and others | 214 | 242 | 4.5E-11 |
| 9 | g618.t1 | ProSitePatterns | PS01358 | Zinc finger RanBP2-type signature. | 218 | 237 | - |
| 15 | g618.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 73 | 159 | 12.953 |
| 14 | g618.t1 | ProSiteProfiles | PS50199 | Zinc finger RanBP2 type profile. | 214 | 243 | 10.557 |
| 11 | g618.t1 | SMART | SM00360 | rrm1_1 | 74 | 155 | 1.3E-12 |
| 10 | g618.t1 | SMART | SM00547 | zf_4 | 216 | 240 | 4.8E-6 |
| 4 | g618.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 71 | 188 | 3.49E-21 |
| 5 | g618.t1 | SUPERFAMILY | SSF90209 | Ran binding protein zinc finger-like | 206 | 244 | 5.34E-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.
