Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative UBX domain-containing protein 4.

Parent gene

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.t2 TTS g8178.t2 28936388 28936388
chr_2 g8178 g8178.t2 isoform g8178.t2 28936516 28937495
chr_2 g8178 g8178.t2 exon g8178.t2.exon1 28936516 28936720
chr_2 g8178 g8178.t2 cds g8178.t2.CDS1 28936516 28936720
chr_2 g8178 g8178.t2 exon g8178.t2.exon2 28936784 28937495
chr_2 g8178 g8178.t2 cds g8178.t2.CDS2 28936784 28937451
chr_2 g8178 g8178.t2 TSS g8178.t2 28938282 28938282

Sequences

>g8178.t2 Gene=g8178 Length=917
GTCAACAACTGCAAAATTTGAAAAAATGGCAGGATGAGCAAGAGATGCTTAAACTACAGG
ATGAACGAAAAAGAGAAAAATTAGCAGCTGCAGAAGCACGCAAAAGAGTTTTACAACAAA
TTGAAGAAGATAAAAAGGAGCGTGCTCGTCGATTTAATTCAACACCTCCGACAAATGAAG
AACCTACGAAAAAAGTCGAAACAATTCCGCAAACATCAGCTACAACTATACCTCCAAATT
CAGCTAGAATTCAATTTAAAAAACCTGATGGAGGAAGTGAAATTGTAACTTTTGATTCGA
ACATACCTTTTGCTGACCTGCATGCATTTGTTAAAACAGATATTCTTAATGGAACAAATA
TTAAGGAGTTTACATTAGCTACGACATTTCCTCGATGTGAATTTTCTCAAACAGATTTTA
ATAAGACTTTGATCGAACTAAATTTGGCACCATCTTCAGTTATATTGATCATTCCTGGAA
AAAGAACAGCAACAAATAATAATAATAATGCAAACACGATATTGCCTACACAAACAGATG
GTAGTATGTTGAGTATGGTTGGAGCATTGATAATGGGACTTTTTTCACCAGTCTTTGCAC
TGTTTACTTATTTGAAAAATTTTATATTTCGCTCGCAAAATAGTAATGAAGAAGAAAGCA
GCAATTATGGACTACAAAAACGAAATGAAGAGACTTTGGCACCAAATGATGCAGCAAAAA
GAAGAAATATGGATAGATTTAATGGTTCGCAGAATCAAGCATCAACATCGTCTCAAGCGG
CTGGCGGTGCAATTCCAAAAACGGGTGCATATAAGCGAATGAAACCTTCGAGCAATATTC
ATCGCCTACATGAAGATTCAGATACTGATAATGAAGAACGAAAAACTTACAACGGAAATA
GTACTCAGCAAATGTAA

>g8178.t2 Gene=g8178 Length=290
MLKLQDERKREKLAAAEARKRVLQQIEEDKKERARRFNSTPPTNEEPTKKVETIPQTSAT
TIPPNSARIQFKKPDGGSEIVTFDSNIPFADLHAFVKTDILNGTNIKEFTLATTFPRCEF
SQTDFNKTLIELNLAPSSVILIIPGKRTATNNNNNANTILPTQTDGSMLSMVGALIMGLF
SPVFALFTYLKNFIFRSQNSNEEESSNYGLQKRNEETLAPNDAAKRRNMDRFNGSQNQAS
TSSQAAGGAIPKTGAYKRMKPSSNIHRLHEDSDTDNEERKTYNGNSTQQM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8178.t2 Coils Coil Coil 1 33 -
4 g8178.t2 Gene3D G3DSA:3.10.20.90 - 59 145 1.6E-16
14 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 24 53 -
16 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 24 39 -
13 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 201 220 -
12 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 233 248 -
15 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 233 290 -
11 g8178.t2 MobiDBLite mobidb-lite consensus disorder prediction 263 280 -
2 g8178.t2 PANTHER PTHR46424 UBX DOMAIN-CONTAINING PROTEIN 4 3 290 2.5E-42
1 g8178.t2 Pfam PF00789 UBX domain 65 142 7.5E-12
7 g8178.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 167 -
8 g8178.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
6 g8178.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 191 290 -
17 g8178.t2 ProSiteProfiles PS50033 UBX domain profile. 62 142 19.179
10 g8178.t2 SMART SM00166 ubx_3 59 144 1.2E-11
3 g8178.t2 SUPERFAMILY SSF54236 Ubiquitin-like 11 143 6.46E-20
9 g8178.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -

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.

Raw TPM values