Gene loci information

Transcript annotation

  • This transcript has been annotated as High mobility group protein DSP1.

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 g8736 g8736.t1 TTS g8736.t1 32704754 32704754
chr_2 g8736 g8736.t1 isoform g8736.t1 32705217 32712442
chr_2 g8736 g8736.t1 exon g8736.t1.exon1 32705217 32705378
chr_2 g8736 g8736.t1 cds g8736.t1.CDS1 32705217 32705378
chr_2 g8736 g8736.t1 exon g8736.t1.exon2 32706256 32706594
chr_2 g8736 g8736.t1 cds g8736.t1.CDS2 32706256 32706594
chr_2 g8736 g8736.t1 exon g8736.t1.exon3 32708014 32708223
chr_2 g8736 g8736.t1 cds g8736.t1.CDS3 32708014 32708223
chr_2 g8736 g8736.t1 exon g8736.t1.exon4 32711918 32712442
chr_2 g8736 g8736.t1 cds g8736.t1.CDS4 32711918 32712442
chr_2 g8736 g8736.t1 TSS g8736.t1 32713132 32713132

Sequences

>g8736.t1 Gene=g8736 Length=1236
ATGTCTGATCAGCACCGCGGAGGTGCGTGGAGTTCACGCGAGGACGCTGTATGGTGGCCG
GGTGCAATCACAGCTGATCAGAGTAATTTGCATCATCAACAAATTATAAATCAGCATCAT
CAGCAAAATCATATGCAACAACAGCAACAGCAGCAGCAACAACAAATTCACCAAGTCGTG
GTGCAGCAGACACAGAACAATACATCAACTTCCAGTGCAGCCTCACAACAGCTTTTCTCA
TATAAAATGGCCAGTAGTTTTCCATCAACTGGCGTTGCAACATCAAATGCGTATGATTAT
CGTTTAGGAATGGGAGCACAAGGTATGAATGTGACTGCTGGTACACAATGGTGGTACACA
GCTGCTGGTCAAAATGCTCTTGAAAATTTGCAAGCTCAACAGCAACAACAACAGCAGCAA
CAGCAGCAGCAACAACAACAACAACAGCAGCAACAGCAACAACAACAGCAACATCATCAG
CATCAATCTCAAAATATACATAATGTACATTCAAATCAATCCTCGAATCAAACTCACGTA
CAACAGAATGCAAATCAAAATAATCAGATTGCGGCAAAGATGAGTAGAGGAAAGGGAGCT
GATGCAAAACCTCGCGGTCGAATGACAGCATACGCATTTTTTGTTCAGACATGTCGTGAA
GAGCACAAGAAAAAACATCCGGAAGAGTCTGTCATATTTGCAGAATTTTCTAGGAAATGT
GCAGAAAGATGGAAGACAATGCTAGATAAAGAGAAGAAACGCTTTCATGAGATGGCAGAA
AAAGACAAACAAAGATATGACATGGAAATGTCAAACTATGTTCCACCGAAAGGAGTTGTT
GTTGGACGTGGCAAGAAACGAAAACATCAGAAAGATCCAAATGCACCAAAACGATCGCTA
TCTGCATTCTTTTGGTTTTGTCATGATGAAAGAAATAAAGTTAAGGCACTTAATCCAGAA
TATGGTGTAGGCGATATAGCTAAGGAACTTGGTCGAAAGTGGTCAGATTGTGATCCAGAA
GTTAAGAGCAAATACGAGGCTATGGCTGATAAAGACAAGCAGAGATATGAAAAAGAAATG
ACGGAATATAAATTGAAATGTAGGAATATCCAGCAGGGCATTATTACACCTAATCAAGTT
AATCATGTACAGCAACCGCAACATATACAAATGCAACAGCAACAGCAGCAAAATGATGAA
GACTCAGGTGATGAAGAAGGTGATGGTGAAGATTAG

>g8736.t1 Gene=g8736 Length=411
MSDQHRGGAWSSREDAVWWPGAITADQSNLHHQQIINQHHQQNHMQQQQQQQQQQIHQVV
VQQTQNNTSTSSAASQQLFSYKMASSFPSTGVATSNAYDYRLGMGAQGMNVTAGTQWWYT
AAGQNALENLQAQQQQQQQQQQQQQQQQQQQQQQQQQHHQHQSQNIHNVHSNQSSNQTHV
QQNANQNNQIAAKMSRGKGADAKPRGRMTAYAFFVQTCREEHKKKHPEESVIFAEFSRKC
AERWKTMLDKEKKRFHEMAEKDKQRYDMEMSNYVPPKGVVVGRGKKRKHQKDPNAPKRSL
SAFFWFCHDERNKVKALNPEYGVGDIAKELGRKWSDCDPEVKSKYEAMADKDKQRYEKEM
TEYKLKCRNIQQGIITPNQVNHVQQPQHIQMQQQQQQNDEDSGDEEGDGED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g8736.t1 CDD cd01390 HMGB-UBF_HMG-box 204 271 4.13742E-20
15 g8736.t1 CDD cd01390 HMGB-UBF_HMG-box 296 360 2.47709E-22
14 g8736.t1 Coils Coil Coil 123 157 -
13 g8736.t1 Coils Coil Coil 353 373 -
11 g8736.t1 Gene3D G3DSA:1.10.30.10 DNA Binding (I) 189 275 1.9E-31
12 g8736.t1 Gene3D G3DSA:1.10.30.10 DNA Binding (I) 281 373 3.4E-28
21 g8736.t1 MobiDBLite mobidb-lite consensus disorder prediction 150 183 -
20 g8736.t1 MobiDBLite mobidb-lite consensus disorder prediction 377 398 -
22 g8736.t1 MobiDBLite mobidb-lite consensus disorder prediction 377 411 -
3 g8736.t1 PANTHER PTHR48112:SF22 HIGH MOBILITY GROUP PROTEIN DSP1 171 404 1.9E-70
4 g8736.t1 PANTHER PTHR48112 HIGH MOBILITY GROUP PROTEIN DSP1 171 404 1.9E-70
7 g8736.t1 PRINTS PR00886 High mobility group (HMG1/HMG2) protein signature 235 257 4.2E-23
8 g8736.t1 PRINTS PR00886 High mobility group (HMG1/HMG2) protein signature 311 329 4.2E-23
6 g8736.t1 PRINTS PR00886 High mobility group (HMG1/HMG2) protein signature 329 348 4.2E-23
5 g8736.t1 PRINTS PR00886 High mobility group (HMG1/HMG2) protein signature 348 368 4.2E-23
1 g8736.t1 Pfam PF09011 HMG-box domain 203 273 3.3E-21
2 g8736.t1 Pfam PF00505 HMG (high mobility group) box 296 364 2.3E-21
19 g8736.t1 ProSitePatterns PS00353 HMG box A DNA-binding domain signature. 236 247 -
23 g8736.t1 ProSiteProfiles PS50118 HMG boxes A and B DNA-binding domains profile. 204 274 16.557
24 g8736.t1 ProSiteProfiles PS50118 HMG boxes A and B DNA-binding domains profile. 296 364 18.788
18 g8736.t1 SMART SM00398 hmgende2 203 275 2.4E-22
17 g8736.t1 SMART SM00398 hmgende2 295 365 2.3E-25
10 g8736.t1 SUPERFAMILY SSF47095 HMG-box 201 276 5.11E-22
9 g8736.t1 SUPERFAMILY SSF47095 HMG-box 282 367 5.89E-26

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:0005634 nucleus CC
GO:0003677 DNA 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