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.t1 TTS g8178.t1 28936388 28936388
chr_2 g8178 g8178.t1 isoform g8178.t1 28936516 28938220
chr_2 g8178 g8178.t1 exon g8178.t1.exon1 28936516 28936720
chr_2 g8178 g8178.t1 cds g8178.t1.CDS1 28936516 28936720
chr_2 g8178 g8178.t1 exon g8178.t1.exon2 28936784 28937891
chr_2 g8178 g8178.t1 cds g8178.t1.CDS2 28936784 28937891
chr_2 g8178 g8178.t1 exon g8178.t1.exon3 28937949 28938083
chr_2 g8178 g8178.t1 cds g8178.t1.CDS3 28937949 28938083
chr_2 g8178 g8178.t1 exon g8178.t1.exon4 28938139 28938220
chr_2 g8178 g8178.t1 cds g8178.t1.CDS4 28938139 28938220
chr_2 g8178 g8178.t1 TSS g8178.t1 28938282 28938282

Sequences

>g8178.t1 Gene=g8178 Length=1530
ATGCAGTGGTTCTCTGGTGACATTGCAGCTGCAGTTAGTTTAGCTAAATCTAAAAGTGCA
ATTTTTGTAGTCTATTGTGAAGGTCAGGATGAAAATTCATCCAGAATGACAGAAATGATG
AATGATGAAAGTGTGAGCTCTAAATTACAATCAGACTCATTTGTCGCTATAAGAATCAAA
AGCGATAAACCAGAATATGAACATTTTCGTAAAATTTATCAACTTGTGCCTATTCCTTCG
CTGTTCTTCATTAAAAATGGAATTCCCATAAAAATTGTGACAAGTGTAATAAAGACAACC
AATGAATTATTAGAAGCTATTGATGGGATTTTAAAGACTCAAATAAATGAGGCAACTATT
AAGACAGTGGAAACAAAAGAGCAAGATCCGAAAATCGTATGTGATGGTGATAGATGTTAT
AAAATAGAATCAGATCAAGCATCATCATCAAAAGAAACTGAAAGTACTGAAAAAAAGTCA
GAAGAAGAAAGTGAAGAGGAGAAACAAGAAAAAGTCAAGAGAGCTCTAAAATTGATAGAA
GAGAAACGCATTGAAAGAATCAAAGAAGAACAACGATTGGAAAAAGAAAGAGAGATACGT
CGAAGACAGGAAGGTCAACAACTGCAAAATTTGAAAAAATGGCAGGATGAGCAAGAGATG
CTTAAACTACAGGATGAACGAAAAAGAGAAAAATTAGCAGCTGCAGAAGCACGCAAAAGA
GTTTTACAACAAATTGAAGAAGATAAAAAGGAGCGTGCTCGTCGATTTAATTCAACACCT
CCGACAAATGAAGAACCTACGAAAAAAGTCGAAACAATTCCGCAAACATCAGCTACAACT
ATACCTCCAAATTCAGCTAGAATTCAATTTAAAAAACCTGATGGAGGAAGTGAAATTGTA
ACTTTTGATTCGAACATACCTTTTGCTGACCTGCATGCATTTGTTAAAACAGATATTCTT
AATGGAACAAATATTAAGGAGTTTACATTAGCTACGACATTTCCTCGATGTGAATTTTCT
CAAACAGATTTTAATAAGACTTTGATCGAACTAAATTTGGCACCATCTTCAGTTATATTG
ATCATTCCTGGAAAAAGAACAGCAACAAATAATAATAATAATGCAAACACGATATTGCCT
ACACAAACAGATGGTAGTATGTTGAGTATGGTTGGAGCATTGATAATGGGACTTTTTTCA
CCAGTCTTTGCACTGTTTACTTATTTGAAAAATTTTATATTTCGCTCGCAAAATAGTAAT
GAAGAAGAAAGCAGCAATTATGGACTACAAAAACGAAATGAAGAGACTTTGGCACCAAAT
GATGCAGCAAAAAGAAGAAATATGGATAGATTTAATGGTTCGCAGAATCAAGCATCAACA
TCGTCTCAAGCGGCTGGCGGTGCAATTCCAAAAACGGGTGCATATAAGCGAATGAAACCT
TCGAGCAATATTCATCGCCTACATGAAGATTCAGATACTGATAATGAAGAACGAAAAACT
TACAACGGAAATAGTACTCAGCAAATGTAA

>g8178.t1 Gene=g8178 Length=509
MQWFSGDIAAAVSLAKSKSAIFVVYCEGQDENSSRMTEMMNDESVSSKLQSDSFVAIRIK
SDKPEYEHFRKIYQLVPIPSLFFIKNGIPIKIVTSVIKTTNELLEAIDGILKTQINEATI
KTVETKEQDPKIVCDGDRCYKIESDQASSSKETESTEKKSEEESEEEKQEKVKRALKLIE
EKRIERIKEEQRLEKEREIRRRQEGQQLQNLKKWQDEQEMLKLQDERKREKLAAAEARKR
VLQQIEEDKKERARRFNSTPPTNEEPTKKVETIPQTSATTIPPNSARIQFKKPDGGSEIV
TFDSNIPFADLHAFVKTDILNGTNIKEFTLATTFPRCEFSQTDFNKTLIELNLAPSSVIL
IIPGKRTATNNNNNANTILPTQTDGSMLSMVGALIMGLFSPVFALFTYLKNFIFRSQNSN
EEESSNYGLQKRNEETLAPNDAAKRRNMDRFNGSQNQASTSSQAAGGAIPKTGAYKRMKP
SSNIHRLHEDSDTDNEERKTYNGNSTQQM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g8178.t1 Coils Coil Coil 150 199 -
5 g8178.t1 Coils Coil Coil 220 252 -
4 g8178.t1 Gene3D G3DSA:3.10.20.90 - 278 364 4.1E-16
12 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 145 171 -
17 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 249 272 -
16 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 420 439 -
14 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 452 467 -
15 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 452 509 -
13 g8178.t1 MobiDBLite mobidb-lite consensus disorder prediction 482 499 -
2 g8178.t1 PANTHER PTHR46424 UBX DOMAIN-CONTAINING PROTEIN 4 1 509 2.7E-89
1 g8178.t1 Pfam PF00789 UBX domain 284 361 1.9E-11
8 g8178.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 386 -
9 g8178.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 387 409 -
7 g8178.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 410 509 -
18 g8178.t1 ProSiteProfiles PS50033 UBX domain profile. 281 361 19.179
11 g8178.t1 SMART SM00166 ubx_3 278 363 1.2E-11
3 g8178.t1 SUPERFAMILY SSF54236 Ubiquitin-like 230 362 2.17E-19
10 g8178.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 387 409 -

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

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.

Raw TPM values