Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein deltex.

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_1 g11999 g11999.t1 TTS g11999.t1 20245748 20245748
chr_1 g11999 g11999.t1 isoform g11999.t1 20245761 20247833
chr_1 g11999 g11999.t1 exon g11999.t1.exon1 20245761 20246061
chr_1 g11999 g11999.t1 cds g11999.t1.CDS1 20245761 20246061
chr_1 g11999 g11999.t1 exon g11999.t1.exon2 20246125 20246267
chr_1 g11999 g11999.t1 cds g11999.t1.CDS2 20246125 20246267
chr_1 g11999 g11999.t1 exon g11999.t1.exon3 20246337 20247833
chr_1 g11999 g11999.t1 cds g11999.t1.CDS3 20246337 20247833
chr_1 g11999 g11999.t1 TSS g11999.t1 20248218 20248218

Sequences

>g11999.t1 Gene=g11999 Length=1941
ATGACTTCCAATAATTGCGTTGTCGTTGTGTGGGAAGTTGAATCGATATTATTGAAAAAG
TATATCCCATACTCGTCTTCCGTTTCGCAGCATCTTGAACGGGCGTATGCGAAAAAATTA
ACGCAAGTCTTTCTTGGTGATTCTGATGCAAGTCTTAATGAGTATTATGTAAATTTACGG
ACAATGAAACAATGCTCAGAGCAACCAGATGCTGAACATCCAATTGTTAATGTTCGCAGA
CAATTTTACAATCCATCGAGTCCTGCGGGCAAAGGTATACGATGGGAATATGCAGGAAAT
TCCACGAGTGAATGGCATCAATATGATCTCGAGCATCAGTGTATAATTGAGGATGCGTGG
ACTAATGGCAATCAACAAATAGATCTTTCTTTATCCTATATTCATATGCCATACATCATT
GACTTTTGCAATATGACACAAACACGTAAGCCAAGTGGTCCGATAAGGCAAATACGTCGA
GTATCACAAGCACCATATCCACTTACAAAACTCCCAAGTCCAATGAATTCACAACAACAG
CAGCAGCAAGCAATATTAAATTCAAAACAACTAACAATGTCCCACGGAACAGGCCTCAAT
GCATCTCGATTATCAATCAACACCAGTCGTAGTCGTCGCAATTATCTTCATCATCAGCAA
ATGCTCTCAACGTCTGCACCTCGATTAAGCAATTATGGTGGCGATACAATTTCACAATCA
GGAAGTACAAGATCGGCACCATCAAATCATGTAACTGGAATTCCGCCAAGCGGTAAACAG
TCAAATAAAATGCAATCATCAAAACCACCAAAACCTACAAAATCAAACAATTCAGAATCA
ACAACAACATCGCCAACGAATCTCGCAAGACAAATTCTCAATAATCTCAATATTTTCTCG
CATCATCATCATCATAATGATAAAAATGCAAATGAATCATCAACAAATCATAAGAAACAT
TTTATTTTAAGTCACAACAGTAATACTGGCCATAAAATGTCAAAGAAAGCACTGTGCAAG
AATTTACACAGTAGCACCTCAACACTTGATATGGAAACTTTGAGTATAAATTCAAGGCGA
CCGAGTGTTGATACCATATCGACTTATTTGAGTAATGGTAGTAAGGGAAGTCGTAGTGGA
TCAGTACGTGGCAAACCCAGTTATGGCTCAGTTTCTGATCTCTTAAATTGTTCATTAAGC
AGCGAAAATGATGATGTATTTCTGTCAAGCCATAGTAGTATATCAAGTAGTATGAGCATG
AATATGATAATTAAAGGCAGCATAGTTGGTGTTGATTCAAGCAGTGAACAGATCTCTAAA
TTTGTAAGTGTTGTGAATGATATACCACAATCAAAGCCATGTCCAATCTGTTTGAATGAA
CTTCATCGCGATAATAGTGCCAAAAATCCAATTGTGTCATTATCGAGATGTCAGCATTTG
ATGCACCTTAATTGCCTTAATGAATTGATTTTAAGTCAAAAAAGTGATTTACAAAAGAAT
CTCTACATTGAATGTCCTACATGTGGAATTATTTATGGTGATAAACGTGGAAATCAACCT
CCAGGAACGATGAGTTGGATAACAATACCAAAAGCATTGCCTGGCCATGAAGATTGCAAT
ACAATTCAAATAATTTACAATATTGCAAGTGGAATCCAAACAGAAAATCATCCGAATCCA
GGCAGAGCATTTTTTGCTGTCGGTTTTCCACGCATTTGTTATCTTCCTGAAAATCCAACT
GGTCGTAAAATTCTGCGCTTTTTGAAAGTAGCTTTTGATAGAGGATTACTTTTTTCAATT
GGACGTTCGGCAACTACAGGACGTGAAGACGTTGTGATTTGGAAAAATGTTGAACATAAA
ACACAATTTTCAATGTATCCAGATCCAAACTATTTACAACGAGTGATGGAACAACTTGTT
CATCTTGGTGTCACAGACTAA

>g11999.t1 Gene=g11999 Length=646
MTSNNCVVVVWEVESILLKKYIPYSSSVSQHLERAYAKKLTQVFLGDSDASLNEYYVNLR
TMKQCSEQPDAEHPIVNVRRQFYNPSSPAGKGIRWEYAGNSTSEWHQYDLEHQCIIEDAW
TNGNQQIDLSLSYIHMPYIIDFCNMTQTRKPSGPIRQIRRVSQAPYPLTKLPSPMNSQQQ
QQQAILNSKQLTMSHGTGLNASRLSINTSRSRRNYLHHQQMLSTSAPRLSNYGGDTISQS
GSTRSAPSNHVTGIPPSGKQSNKMQSSKPPKPTKSNNSESTTTSPTNLARQILNNLNIFS
HHHHHNDKNANESSTNHKKHFILSHNSNTGHKMSKKALCKNLHSSTSTLDMETLSINSRR
PSVDTISTYLSNGSKGSRSGSVRGKPSYGSVSDLLNCSLSSENDDVFLSSHSSISSSMSM
NMIIKGSIVGVDSSSEQISKFVSVVNDIPQSKPCPICLNELHRDNSAKNPIVSLSRCQHL
MHLNCLNELILSQKSDLQKNLYIECPTCGIIYGDKRGNQPPGTMSWITIPKALPGHEDCN
TIQIIYNIASGIQTENHPNPGRAFFAVGFPRICYLPENPTGRKILRFLKVAFDRGLLFSI
GRSATTGREDVVIWKNVEHKTQFSMYPDPNYLQRVMEQLVHLGVTD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11999.t1 CDD cd09633 Deltex_C 517 643 1.67996E-69
11 g11999.t1 Gene3D G3DSA:3.30.720.50 - 8 168 2.0E-53
12 g11999.t1 Gene3D G3DSA:3.30.720.50 - 11 80 2.0E-53
13 g11999.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 434 512 6.5E-12
10 g11999.t1 Gene3D G3DSA:3.30.390.130 - 515 645 1.3E-48
18 g11999.t1 MobiDBLite mobidb-lite consensus disorder prediction 237 285 -
5 g11999.t1 PANTHER PTHR12622:SF5 E3 UBIQUITIN-PROTEIN LIGASE DTX4 7 645 6.4E-94
6 g11999.t1 PANTHER PTHR12622 DELTEX-RELATED 7 645 6.4E-94
2 g11999.t1 Pfam PF02825 WWE domain 9 80 2.4E-10
1 g11999.t1 Pfam PF02825 WWE domain 95 160 1.2E-14
4 g11999.t1 Pfam PF13639 Ring finger domain 454 508 1.7E-6
3 g11999.t1 Pfam PF18102 Deltex C-terminal domain 516 644 1.2E-44
20 g11999.t1 ProSiteProfiles PS50918 WWE domain profile. 1 80 10.63
21 g11999.t1 ProSiteProfiles PS50918 WWE domain profile. 81 160 21.238
19 g11999.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 454 508 10.498
16 g11999.t1 SMART SM00678 deltex 6 88 8.2E-12
15 g11999.t1 SMART SM00678 deltex 90 168 7.5E-22
17 g11999.t1 SMART SM00184 ring_2 454 508 3.1E-5
9 g11999.t1 SUPERFAMILY SSF117839 WWE domain 8 92 9.81E-15
8 g11999.t1 SUPERFAMILY SSF117839 WWE domain 90 170 2.09E-23
7 g11999.t1 SUPERFAMILY SSF57850 RING/U-box 448 531 2.25E-13

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:0016567 protein ubiquitination BP
GO:0008270 zinc ion binding MF
GO:0007219 Notch signaling pathway BP

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