General information for g1810.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ran-binding protein 3.
Parent gene
- The parent gene g1810 is located on chr_3: 13137940..13139252 (+ 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 | g1810 | g1810.t6 | TSS | g1810.t6 | 13137381 | 13137381 |
| chr_3 | g1810 | g1810.t6 | isoform | g1810.t6 | 13137483 | 13139252 |
| chr_3 | g1810 | g1810.t6 | exon | g1810.t6.exon1 | 13137483 | 13137501 |
| chr_3 | g1810 | g1810.t6 | cds | g1810.t6.CDS1 | 13137483 | 13137501 |
| chr_3 | g1810 | g1810.t6 | exon | g1810.t6.exon2 | 13137572 | 13137888 |
| chr_3 | g1810 | g1810.t6 | cds | g1810.t6.CDS2 | 13137572 | 13137888 |
| chr_3 | g1810 | g1810.t6 | exon | g1810.t6.exon3 | 13137946 | 13138696 |
| chr_3 | g1810 | g1810.t6 | cds | g1810.t6.CDS3 | 13137946 | 13138695 |
| chr_3 | g1810 | g1810.t6 | exon | g1810.t6.exon4 | 13138815 | 13139252 |
| chr_3 | g1810 | g1810.t6 | TTS | g1810.t6 | 13139777 | 13139777 |
Sequences
>g1810.t6 Gene=g1810 Length=1525
ATGGACAATAACCAAGCAGGATCTAGAAAATTGTTCTTAAAACCAGCTAAATCGGGCTTA
CAAAAAACAGAACAGCAACAACAACAAACAAACGGAAGCAGTTCATCTGAAAATGGAAAT
ATATTCAATCTGAGTAACAATCCTTTCCTTAAATGTGAGGAAGATATAGAAACTAAAAAT
AATGAAGAAAAAGTTTCTAAAGAAACTGATAATGCTGATATTAAAGCAAAAGATTTGTTT
AAGCCAGTTAGTACAAATCTCTTCAAAAATGCCACAACATTATCAGAAAATTCCAATTTT
GTGTTTGGTCAAAATCTCCATGAAAGAGTAGTTATTGATAAAACATCAACCACTGCAGCA
TCTACAGAAAGTGAAAACAAAAGCAATGATGAAAAAGATGAAAAGACAAACAAACTACTT
TTTTCAAGTGCCCTTTCGCAACAGCCGACAGAAAAAACAGAGCGAAGGAATAATGATGAT
AATGCCGAGAACAATACACAGCCAATATCGACGAAAAAAACTGATGATCAGTCTGAAGAA
AATTTAAGTCTCATTGAAGCGGCTAGGAGATATGAAGAAATTAAAAGTGCACAGAAAAGA
AAATTTGAAGAGGTAGAAGTGATAACTGGTGAGGAAGATGACAAAAATATTTTAGAAATG
AACTGTAGACTGTTTACATTCGATAAAAATAATTGGGAAGAAAGAGGTCGTGGAACTCTA
CGTCTGAATGATTGCAAAAATAGTGCTCGTGTTGTATTTCGTGCGTCAGGTAGTTTACGT
TTATTACTTAATACAAAAGTATGGAAAGACCAGTTATGCGAGCTGGCCAATTCAAAGAGT
TTGAAGCTTACGGCTATTGATTCTAATGGACTAGTAAAAATTTACCTTGTAACGGGCAGA
ATTGAGGATATCGACAATCTATATCATGCTTTAAGCATTCGTATTAAGAGGGAAAAGGAC
CGAACAGTACACAAAACAACTGAAAATGAGGAAGAAGTTGATGAAACTACTGAGAATGCC
AATGTATCAAATAATGACGACCATAGTTTGGAGCCAGTTCCAAAAAAAATTGCAACAACT
GAATGAATTGATTGTACAATCCATAAGAGTATGTAATTTAACTTTTTTTTAAAGTTAATG
AATTTTTAACTCATTCACATCATTTTAATCACAGATTTTAGAATTTTTCATAATTATAAG
AATTTTAAGAGATAAACTGATGCTTAATAAATATTATTTTATTTGCTTCAGATTCTAAGA
ATTGTTTGTCTGTTTTTATGAACAAATACCTATAAACGATATGCGTTGCTTGAAAAAACT
TTCTTGAATGACTGTTGTAATCATGCATACATGTTAATGTTTTCTTTTTCTTCAAAATTC
AACGTGTGAAGACAAACACAATTAATTAATGAGTTTTGAATGTTGTAGATTTTTAAATGA
ACTTGACAGACTTTAATTTTGATGATCGTATAAACAGGTTTAACTAATGAGTTCAGAAGA
AGAAAAGGCATATTTAAGTGTCAGC
>g1810.t6 Gene=g1810 Length=361
MDNNQAGSRKLFLKPAKSGLQKTEQQQQQTNGSSSSENGNIFNLSNNPFLKCEEDIETKN
NEEKVSKETDNADIKAKDLFKPVSTNLFKNATTLSENSNFVFGQNLHERVVIDKTSTTAA
STESENKSNDEKDEKTNKLLFSSALSQQPTEKTERRNNDDNAENNTQPISTKKTDDQSEE
NLSLIEAARRYEEIKSAQKRKFEEVEVITGEEDDKNILEMNCRLFTFDKNNWEERGRGTL
RLNDCKNSARVVFRASGSLRLLLNTKVWKDQLCELANSKSLKLTAIDSNGLVKIYLVTGR
IEDIDNLYHALSIRIKREKDRTVHKTTENEEEVDETTENANVSNNDDHSLEPVPKKIATT
E
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1810.t6 | CDD | cd13180 | RanBD_RanBP3 | 209 | 315 | 3.02008E-44 |
| 5 | g1810.t6 | Gene3D | G3DSA:2.30.29.30 | - | 135 | 316 | 6.5E-31 |
| 9 | g1810.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 41 | - |
| 8 | g1810.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 19 | 41 | - |
| 11 | g1810.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 114 | 180 | - |
| 10 | g1810.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 361 | - |
| 2 | g1810.t6 | PANTHER | PTHR23138 | RAN BINDING PROTEIN | 57 | 349 | 7.6E-45 |
| 3 | g1810.t6 | PANTHER | PTHR23138:SF151 | RAN-BINDING PROTEIN 3A-RELATED | 57 | 349 | 7.6E-45 |
| 1 | g1810.t6 | Pfam | PF00638 | RanBP1 domain | 206 | 271 | 2.6E-9 |
| 12 | g1810.t6 | ProSiteProfiles | PS50196 | Ran binding domain type 1 profile. | 190 | 270 | 13.478 |
| 7 | g1810.t6 | SMART | SM00160 | ranbd_3 | 196 | 314 | 3.0E-8 |
| 4 | g1810.t6 | SUPERFAMILY | SSF50729 | PH domain-like | 200 | 312 | 4.51E-27 |
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:0046907 | intracellular transport | BP |
KEGG
Orthology
- This transcript has been annotated with K15304 (Ran-binding protein 3)
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.
