General information for g5790.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative UBX domain-containing protein 6.
Parent gene
- The parent gene g5790 is located on chr_2: 11944509..11945661 (+ 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_2 | g5790 | g5790.t1 | TSS | g5790.t1 | 11943694 | 11943694 |
| chr_2 | g5790 | g5790.t1 | isoform | g5790.t1 | 11944127 | 11945661 |
| chr_2 | g5790 | g5790.t1 | exon | g5790.t1.exon1 | 11944127 | 11945064 |
| chr_2 | g5790 | g5790.t1 | cds | g5790.t1.CDS1 | 11944127 | 11945064 |
| chr_2 | g5790 | g5790.t1 | exon | g5790.t1.exon2 | 11945153 | 11945282 |
| chr_2 | g5790 | g5790.t1 | cds | g5790.t1.CDS2 | 11945153 | 11945282 |
| chr_2 | g5790 | g5790.t1 | exon | g5790.t1.exon3 | 11945341 | 11945489 |
| chr_2 | g5790 | g5790.t1 | cds | g5790.t1.CDS3 | 11945341 | 11945489 |
| chr_2 | g5790 | g5790.t1 | exon | g5790.t1.exon4 | 11945559 | 11945661 |
| chr_2 | g5790 | g5790.t1 | cds | g5790.t1.CDS4 | 11945559 | 11945661 |
| chr_2 | g5790 | g5790.t1 | TTS | g5790.t1 | 11945754 | 11945754 |
Sequences
>g5790.t1 Gene=g5790 Length=1320
ATGAGTTCGGTAGGAGCTAAAGTTAAAAAGTTTTTTGCTAAGAAAAAGTCGGACGCGAAA
TTTGCTAAAGCGGGACCTGGAAGAAAATTGACAGGTGATGATGGTGGAAGTAGTAGCAGA
GATAGTAAACCCAAAGATAAAGATGCATATGTCCCTATAAAAAGAGATGATTTGACTGAT
GAAATGAAGAAAGCTCGTGATGCAGCATTGGAAAGAATGAATAAAACTTCTAATACACCA
TCTTTTGATCTTTCGCTTAAAGCTATAAAAGAAAAAGCTCGAAAAGAGCTTGAAGAAGAG
AAAGTAAGAAAAGTTGAAAATGAAATGAGTAATTTAAAAATAAATGAAGAACCGAAACAA
GACGAGAACACCATTGATATAAATTTTACATGTTCTCTTATATCTGATGAAATACTACCT
AAAAAGGAATGGAAACAAAAAATCAAAGATTTCTTACATGAGCAACTTCAACTTGCATTA
AGCAATAGCACTGATCATCTTGATCCAGGAATTACATCTTGTCTTATTATAAAGAGTTGC
AATCCTATCGAGCGTTCACAAGATTGCGTTGAGACACTCAAAAAGTATCTCTCAAATATT
ATTCAAGAACCATCGGAAGTTAAATTTCATAAAATTCGTATGACTAACAGAATTTTTTGT
GATAAAGTCGCCAACGTTGAAGGCTCATCGGAATTTTTAAAAAATGCTGGCTTTAGTGAG
CAGGTCATTGATGGTGAAAGTTTCCTTGTTTGGTCGCCAGAAACATCAATAGAACATCTT
TTAAAACAAATCGAATATTTAAATGAATGCGAACCAATTCAACTAGAACTTGATCGTAAC
ATTCAAGTTTTGCTACCTTCGCAAAATAATCAGCCTTCGCTATCTCAAGATTTTTTCAAG
CTTACCGCAGAAGAACTTAAGAGAGAACAAACAAATAAGACTTCAGCCGTTGAAGATGCT
ATGGTTTTAAAAACAAAGGCAATGCGTGAAAAAGAGCAAGAAAGATTTGTTAAAAAATTC
AAATACTCGGTTATTAGAGTACGTTTTCCTGATGGCCTATTCTTACAAGGAACATTTTCG
GTTTATGAAAAACTATCTAATATATATGAGTTTGTTGCTAGTCAATTGCAACATGAATCT
GCTGAATTTTCTTTACTTTCACCTGATGGTGTAAAATTCACTGATGAAGATCAAGGAAAG
ACACTTTATGCATTAAGATTAGTCCCAAATTGCATTCTGAAGTTTACGTATGAAAATGAG
TCTAAATCATTCAACGAATATCTAAAAGATGAAGCGTTAATGCTTGTTAGACCAGTATAA
>g5790.t1 Gene=g5790 Length=439
MSSVGAKVKKFFAKKKSDAKFAKAGPGRKLTGDDGGSSSRDSKPKDKDAYVPIKRDDLTD
EMKKARDAALERMNKTSNTPSFDLSLKAIKEKARKELEEEKVRKVENEMSNLKINEEPKQ
DENTIDINFTCSLISDEILPKKEWKQKIKDFLHEQLQLALSNSTDHLDPGITSCLIIKSC
NPIERSQDCVETLKKYLSNIIQEPSEVKFHKIRMTNRIFCDKVANVEGSSEFLKNAGFSE
QVIDGESFLVWSPETSIEHLLKQIEYLNECEPIQLELDRNIQVLLPSQNNQPSLSQDFFK
LTAEELKREQTNKTSAVEDAMVLKTKAMREKEQERFVKKFKYSVIRVRFPDGLFLQGTFS
VYEKLSNIYEFVASQLQHESAEFSLLSPDGVKFTDEDQGKTLYALRLVPNCILKFTYENE
SKSFNEYLKDEALMLVRPV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5790.t1 | CDD | cd10460 | PUB_UBXD1 | 174 | 260 | 7.73101E-33 |
| 9 | g5790.t1 | CDD | cd16119 | UBX_UBXN6 | 342 | 416 | 8.87884E-30 |
| 8 | g5790.t1 | Coils | Coil | Coil | 87 | 115 | - |
| 7 | g5790.t1 | Gene3D | G3DSA:1.20.58.2190 | - | 174 | 269 | 6.7E-22 |
| 6 | g5790.t1 | Gene3D | G3DSA:3.10.20.90 | - | 335 | 426 | 1.2E-12 |
| 13 | g5790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 61 | - |
| 14 | g5790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 34 | 61 | - |
| 3 | g5790.t1 | PANTHER | PTHR23153 | UBX-RELATED | 9 | 436 | 4.6E-110 |
| 1 | g5790.t1 | Pfam | PF09409 | PUB domain | 184 | 258 | 2.3E-21 |
| 2 | g5790.t1 | Pfam | PF00789 | UBX domain | 342 | 410 | 8.6E-10 |
| 15 | g5790.t1 | ProSiteProfiles | PS50033 | UBX domain profile. | 338 | 415 | 12.553 |
| 11 | g5790.t1 | SMART | SM00580 | PGNneu | 188 | 252 | 1.2E-10 |
| 12 | g5790.t1 | SMART | SM00166 | ubx_3 | 334 | 415 | 0.0042 |
| 5 | g5790.t1 | SUPERFAMILY | SSF143503 | PUG domain-like | 168 | 280 | 6.93E-28 |
| 4 | g5790.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 308 | 415 | 1.14E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5790/g5790.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5790.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14011 (UBX domain-containing protein 6)
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.
