General information for g8178.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative UBX domain-containing protein 4.
Parent gene
- The parent gene g8178 is located on chr_2: 28938136..28945136 (- 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 | g8178 | g8178.t3 | TTS | g8178.t3 | 28936388 | 28936388 |
| chr_2 | g8178 | g8178.t3 | isoform | g8178.t3 | 28936516 | 28938220 |
| chr_2 | g8178 | g8178.t3 | exon | g8178.t3.exon1 | 28936516 | 28936720 |
| chr_2 | g8178 | g8178.t3 | cds | g8178.t3.CDS1 | 28936516 | 28936720 |
| chr_2 | g8178 | g8178.t3 | exon | g8178.t3.exon2 | 28936784 | 28937891 |
| chr_2 | g8178 | g8178.t3 | cds | g8178.t3.CDS2 | 28936784 | 28937891 |
| chr_2 | g8178 | g8178.t3 | exon | g8178.t3.exon3 | 28937945 | 28938083 |
| chr_2 | g8178 | g8178.t3 | cds | g8178.t3.CDS3 | 28937945 | 28937969 |
| chr_2 | g8178 | g8178.t3 | exon | g8178.t3.exon4 | 28938139 | 28938220 |
| chr_2 | g8178 | g8178.t3 | TSS | g8178.t3 | 28938282 | 28938282 |
Sequences
>g8178.t3 Gene=g8178 Length=1534
ATGCAGTGGTTCTCTGGTGACATTGCAGCTGCAGTTAGTTTAGCTAAATCTAAAAGTGCA
ATTTTTGTAGTCTATTGTGAAGGTCAGGATGAAAATTCATCCAGAATGACAGAAATGATG
AATGATGAAAGTGTGAGCTCTAAATTACAATCAGACTCATTTGTCGCTATAAGAATCAAA
AGCGATAAACCAGAATATGAACATTTTCGTAAAATTTGTTAATCAACTTGTGCCTATTCC
TTCGCTGTTCTTCATTAAAAATGGAATTCCCATAAAAATTGTGACAAGTGTAATAAAGAC
AACCAATGAATTATTAGAAGCTATTGATGGGATTTTAAAGACTCAAATAAATGAGGCAAC
TATTAAGACAGTGGAAACAAAAGAGCAAGATCCGAAAATCGTATGTGATGGTGATAGATG
TTATAAAATAGAATCAGATCAAGCATCATCATCAAAAGAAACTGAAAGTACTGAAAAAAA
GTCAGAAGAAGAAAGTGAAGAGGAGAAACAAGAAAAAGTCAAGAGAGCTCTAAAATTGAT
AGAAGAGAAACGCATTGAAAGAATCAAAGAAGAACAACGATTGGAAAAAGAAAGAGAGAT
ACGTCGAAGACAGGAAGGTCAACAACTGCAAAATTTGAAAAAATGGCAGGATGAGCAAGA
GATGCTTAAACTACAGGATGAACGAAAAAGAGAAAAATTAGCAGCTGCAGAAGCACGCAA
AAGAGTTTTACAACAAATTGAAGAAGATAAAAAGGAGCGTGCTCGTCGATTTAATTCAAC
ACCTCCGACAAATGAAGAACCTACGAAAAAAGTCGAAACAATTCCGCAAACATCAGCTAC
AACTATACCTCCAAATTCAGCTAGAATTCAATTTAAAAAACCTGATGGAGGAAGTGAAAT
TGTAACTTTTGATTCGAACATACCTTTTGCTGACCTGCATGCATTTGTTAAAACAGATAT
TCTTAATGGAACAAATATTAAGGAGTTTACATTAGCTACGACATTTCCTCGATGTGAATT
TTCTCAAACAGATTTTAATAAGACTTTGATCGAACTAAATTTGGCACCATCTTCAGTTAT
ATTGATCATTCCTGGAAAAAGAACAGCAACAAATAATAATAATAATGCAAACACGATATT
GCCTACACAAACAGATGGTAGTATGTTGAGTATGGTTGGAGCATTGATAATGGGACTTTT
TTCACCAGTCTTTGCACTGTTTACTTATTTGAAAAATTTTATATTTCGCTCGCAAAATAG
TAATGAAGAAGAAAGCAGCAATTATGGACTACAAAAACGAAATGAAGAGACTTTGGCACC
AAATGATGCAGCAAAAAGAAGAAATATGGATAGATTTAATGGTTCGCAGAATCAAGCATC
AACATCGTCTCAAGCGGCTGGCGGTGCAATTCCAAAAACGGGTGCATATAAGCGAATGAA
ACCTTCGAGCAATATTCATCGCCTACATGAAGATTCAGATACTGATAATGAAGAACGAAA
AACTTACAACGGAAATAGTACTCAGCAAATGTAA
>g8178.t3 Gene=g8178 Length=445
MNIFVKFVNQLVPIPSLFFIKNGIPIKIVTSVIKTTNELLEAIDGILKTQINEATIKTVE
TKEQDPKIVCDGDRCYKIESDQASSSKETESTEKKSEEESEEEKQEKVKRALKLIEEKRI
ERIKEEQRLEKEREIRRRQEGQQLQNLKKWQDEQEMLKLQDERKREKLAAAEARKRVLQQ
IEEDKKERARRFNSTPPTNEEPTKKVETIPQTSATTIPPNSARIQFKKPDGGSEIVTFDS
NIPFADLHAFVKTDILNGTNIKEFTLATTFPRCEFSQTDFNKTLIELNLAPSSVILIIPG
KRTATNNNNNANTILPTQTDGSMLSMVGALIMGLFSPVFALFTYLKNFIFRSQNSNEEES
SNYGLQKRNEETLAPNDAAKRRNMDRFNGSQNQASTSSQAAGGAIPKTGAYKRMKPSSNI
HRLHEDSDTDNEERKTYNGNSTQQM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8178.t3 | Coils | Coil | Coil | 86 | 135 | - |
| 5 | g8178.t3 | Coils | Coil | Coil | 156 | 188 | - |
| 4 | g8178.t3 | Gene3D | G3DSA:3.10.20.90 | - | 214 | 300 | 3.3E-16 |
| 17 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 107 | - |
| 15 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 185 | 208 | - |
| 16 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 356 | 375 | - |
| 13 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 388 | 403 | - |
| 14 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 388 | 445 | - |
| 12 | g8178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 418 | 435 | - |
| 2 | g8178.t3 | PANTHER | PTHR46424 | UBX DOMAIN-CONTAINING PROTEIN 4 | 11 | 445 | 4.1E-62 |
| 1 | g8178.t3 | Pfam | PF00789 | UBX domain | 220 | 297 | 1.6E-11 |
| 8 | g8178.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 322 | - |
| 9 | g8178.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 345 | - |
| 7 | g8178.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 346 | 445 | - |
| 18 | g8178.t3 | ProSiteProfiles | PS50033 | UBX domain profile. | 217 | 297 | 19.179 |
| 11 | g8178.t3 | SMART | SM00166 | ubx_3 | 214 | 299 | 1.2E-11 |
| 3 | g8178.t3 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 166 | 298 | 1.68E-19 |
| 10 | g8178.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 345 | - |
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:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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