General information for g3048.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RUN and FYVE domain-containing protein 2.
Parent gene
- The parent gene g3048 is located on chr_3: 22334971..22336888 (- 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 | g3048 | g3048.t1 | TTS | g3048.t1 | 22334504 | 22334504 |
| chr_3 | g3048 | g3048.t1 | isoform | g3048.t1 | 22334971 | 22336888 |
| chr_3 | g3048 | g3048.t1 | exon | g3048.t1.exon1 | 22334971 | 22335336 |
| chr_3 | g3048 | g3048.t1 | cds | g3048.t1.CDS1 | 22334971 | 22335336 |
| chr_3 | g3048 | g3048.t1 | exon | g3048.t1.exon2 | 22335444 | 22335846 |
| chr_3 | g3048 | g3048.t1 | cds | g3048.t1.CDS2 | 22335444 | 22335846 |
| chr_3 | g3048 | g3048.t1 | exon | g3048.t1.exon3 | 22335910 | 22336570 |
| chr_3 | g3048 | g3048.t1 | cds | g3048.t1.CDS3 | 22335910 | 22336570 |
| chr_3 | g3048 | g3048.t1 | exon | g3048.t1.exon4 | 22336879 | 22336888 |
| chr_3 | g3048 | g3048.t1 | cds | g3048.t1.CDS4 | 22336879 | 22336888 |
| chr_3 | g3048 | g3048.t1 | TSS | g3048.t1 | NA | NA |
Sequences
>g3048.t1 Gene=g3048 Length=1440
ATGTTTTTTGCGCGTGATCCTGCTGCTATTGAGCGATCGAATTTGGTAAACATTTGCAAA
TTAGTAGTGAAAGAATTGCTTGAACAATCACTTCGATATGGTCGTCAATTAGATTCAGAT
CATCTTCCATTGCAACATTTTTTCATCATTTTGGAGCACATTTTAAAACATGGATTGAAG
CCGAAAAAAGGTATATTAGGCCCGAAAAAAGAATTATGGGATTTGTTGCAGAGCACTGAG
AAATATTGTCCAGAAGCTCAAGATGTGACTTCAACTATTCGTGACTTGCCGACTGTACGC
ACTCAAACTGGTCGATCTCGTGCATGGCTTCGATTGGCTTTAATGCAAAAGAAACTTGCT
GATTACTTGCAAGCATTGATTGAGCACAAAAATGAAATTCTTGTGGAATATTATGAACCA
CATGCATTAATGCTCAGTGATGAAATCGTAGTGATTATGGGAATATTGGTTGGACTGAAT
GTGATTGACTGTAATTTATGTGTGAAGGGTGAAGATTTGGATTCACAGCAAGGAGTCATT
GATTTTTCGCTGTATCTTCGATCAAGTTCACGAACAAGTCCTGAAAATGACCAACCAGCT
ATTGAAGGTGGTAATATGACAGCTGTTTTAGATCAAAAAAATTATATTGAGGAACTAAAT
CGACATTTGAATGCAACAGTTGCAAATCTTCAACAAAAAGTAGAACAGCTAACTACGACA
AATGCTTTAATGAAAGAAGATCTTGCAATTGCAAGAAATAGTTTACTCACACTACAAGCT
GAGAATAGCGCACTACGGCAAAATCAAAATGCTGCCAATCAGCAAATTGTCGATAGAGCA
AATGTGTTGGATCGTGTCGATCCTGAAATGGCAGAAACATTAGCTGATGAGCGTAAGAAG
AGACAAGAGGTTGAAAGAGAATTGGAATTGCAAGTGTGCCTAAAAGCTGAAACTGAAATG
GCAATGAAGTTACTTGAAAAGGACATTCATGAAAAACAAGACACTATTATTTCACTAAGA
CGACAACTTGAAGATATTAAACAAATCAATTTGGAAATGTATAAGAAATTGCAGGAATGC
GAATTTGAATTAACTCAAAAAGGCGAGATGGTAGAGCGTTTGCAAGCCAAAGCATCGAGT
ATTGGTAGAATTTTGACCAATTTGGAGAAAAAGTATAGCAGTTCACATGGAAATGAAAAT
GATATGAAAAAATCACCCTCGGGATCACAATTGGGTCATCCACCAAATAAACGCGCGTAT
CTTAAAATACAACCCATTCCACCATTTAATGCAAATAAGCTTACTAAATCACCATCATCA
ATTGAACCTACCATTTCTACACCAGATTCAACTAGTACTGCTATTGTAGAAGTTGAAGAT
GATAATGATAAGGCTAAAACACCAGTTGATGAAAATGCGAAGGAGAAAAATGAAGAATAA
>g3048.t1 Gene=g3048 Length=479
MFFARDPAAIERSNLVNICKLVVKELLEQSLRYGRQLDSDHLPLQHFFIILEHILKHGLK
PKKGILGPKKELWDLLQSTEKYCPEAQDVTSTIRDLPTVRTQTGRSRAWLRLALMQKKLA
DYLQALIEHKNEILVEYYEPHALMLSDEIVVIMGILVGLNVIDCNLCVKGEDLDSQQGVI
DFSLYLRSSSRTSPENDQPAIEGGNMTAVLDQKNYIEELNRHLNATVANLQQKVEQLTTT
NALMKEDLAIARNSLLTLQAENSALRQNQNAANQQIVDRANVLDRVDPEMAETLADERKK
RQEVERELELQVCLKAETEMAMKLLEKDIHEKQDTIISLRRQLEDIKQINLEMYKKLQEC
EFELTQKGEMVERLQAKASSIGRILTNLEKKYSSSHGNENDMKKSPSGSQLGHPPNKRAY
LKIQPIPPFNANKLTKSPSSIEPTISTPDSTSTAIVEVEDDNDKAKTPVDENAKEKNEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3048.t1 | Coils | Coil | Coil | 112 | 132 | - |
| 9 | g3048.t1 | Coils | Coil | Coil | 216 | 275 | - |
| 8 | g3048.t1 | Coils | Coil | Coil | 315 | 349 | - |
| 7 | g3048.t1 | Coils | Coil | Coil | 371 | 391 | - |
| 5 | g3048.t1 | Gene3D | G3DSA:1.20.58.900 | - | 4 | 181 | 4.4E-74 |
| 12 | g3048.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 412 | - |
| 14 | g3048.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 413 | - |
| 11 | g3048.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 431 | 455 | - |
| 15 | g3048.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 431 | 479 | - |
| 13 | g3048.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 457 | 479 | - |
| 2 | g3048.t1 | PANTHER | PTHR45956 | RUN AND FYVE DOMAIN-CONTAINING PROTEIN 2-LIKE PROTEIN | 4 | 414 | 1.1E-187 |
| 3 | g3048.t1 | PANTHER | PTHR45956:SF6 | RUN AND FYVE DOMAIN-CONTAINING PROTEIN 2-LIKE PROTEIN | 4 | 414 | 1.1E-187 |
| 1 | g3048.t1 | Pfam | PF02759 | RUN domain | 47 | 169 | 1.3E-29 |
| 16 | g3048.t1 | ProSiteProfiles | PS50826 | RUN domain profile. | 38 | 171 | 28.59 |
| 10 | g3048.t1 | SMART | SM00593 | 893paper3 | 106 | 169 | 3.6E-21 |
| 4 | g3048.t1 | SUPERFAMILY | SSF140741 | RUN domain-like | 11 | 175 | 3.27E-45 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12482 (RUN and FYVE domain-containing protein 1/2)
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.
