Gene loci information

Transcript annotation

  • This transcript has been annotated as Proteasome subunit alpha type-5.

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 g5573 g5573.t1 TTS g5573.t1 10347276 10347276
chr_2 g5573 g5573.t1 isoform g5573.t1 10347358 10348952
chr_2 g5573 g5573.t1 exon g5573.t1.exon1 10347358 10347953
chr_2 g5573 g5573.t1 cds g5573.t1.CDS1 10347358 10347953
chr_2 g5573 g5573.t1 exon g5573.t1.exon2 10348011 10348142
chr_2 g5573 g5573.t1 cds g5573.t1.CDS2 10348011 10348142
chr_2 g5573 g5573.t1 TSS g5573.t1 10348395 10348395
chr_2 g5573 g5573.t1 exon g5573.t1.exon3 10348590 10348817
chr_2 g5573 g5573.t1 cds g5573.t1.CDS3 10348590 10348817
chr_2 g5573 g5573.t1 exon g5573.t1.exon4 10348871 10348952
chr_2 g5573 g5573.t1 cds g5573.t1.CDS4 10348871 10348952

Sequences

>g5573.t1 Gene=g5573 Length=1038
ATGAGCGAAAATACGCGAATGACAATTGATGAAGCTAGAAAATATAAATTCAAGGCTGCA
GCTTTTCTTATTGGTGTTGCAGGCATTTCTGCGGCTATTGGGTTTTCGAGAACACTTGCA
ATGGCTAAGAAAAAAGACACAATGTATTTTACAAAAGGAATGCAAGAATCACCAGATTTA
GCAGGAGTTCAATTGGCAATGAAGGCTTTAGGCTACGGAACGTTATATGCAGTAATAGGC
ACAGGATCATTATTTTATGGAATATGGAAATTATCGGGAGCAAAAAATCTCGAAGAGTTC
AGAATCAAATTGTTCCTTACACGTTCAGAATATGATAGAGGTGTCAACACTTACTCACCA
GAAGGAAGATTACTACAAGTTGAATATGCTATTGAAGCCATTAAATTGGGTAGCACTGCT
ATCGGTATCAGTACATCAGAGGGTGTAGTTATGGTTGTTGAAAAGCGTATTACATCACCA
TTGATGGAACCTTCTAAAGTTGAGAAAATATTTGAAGTAGATCGTCATATTGGCTGTGCT
ACATCTGGATTGATGGCTGATTCAAGAACTCTTTTGGAACGCGCAAGAGTTGAAGCTCAA
AATCATTGGTTTGTTTATAATGAACCAATGTATGTTGAGTCATGTGCTAGAGCAGTTTCA
AATTTAGCTATTCAATTTGGAGATTCATCAGATGACAGCGGTTCGGCAATGAGTCGACCT
TTCGGTGTGGCAATTTTATTTGCTGGAGTTGATAATAATGTTCCACAATTATATCATATG
GATCCATCTGGCACTTTGTTGAGATATGATGCGAAAGCAATTGGATCGGGTAGTGAAGGA
GCTCAGCAGCATTTGCAGGAAATTTACTCAAGCTCATTAACATTGAAAGAGGCCGTCTCA
AAAGCACTAGAAACTCTTAAGCAAGTAATGGAAGAAAAATTGAGTTCAACAAATGTAGAA
GTTATGACAATGACTCCAAAAGATCTCTTCTACATGTATACAAAAGAAGAGGTTGAAGCT
GTAATTGCTGATTTATAA

>g5573.t1 Gene=g5573 Length=345
MSENTRMTIDEARKYKFKAAAFLIGVAGISAAIGFSRTLAMAKKKDTMYFTKGMQESPDL
AGVQLAMKALGYGTLYAVIGTGSLFYGIWKLSGAKNLEEFRIKLFLTRSEYDRGVNTYSP
EGRLLQVEYAIEAIKLGSTAIGISTSEGVVMVVEKRITSPLMEPSKVEKIFEVDRHIGCA
TSGLMADSRTLLERARVEAQNHWFVYNEPMYVESCARAVSNLAIQFGDSSDDSGSAMSRP
FGVAILFAGVDNNVPQLYHMDPSGTLLRYDAKAIGSGSEGAQQHLQEIYSSSLTLKEAVS
KALETLKQVMEEKLSSTNVEVMTMTPKDLFYMYTKEEVEAVIADL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g5573.t1 CDD cd03753 proteasome_alpha_type_5 111 324 6.69051E-140
7 g5573.t1 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate 104 345 2.1E-86
4 g5573.t1 PANTHER PTHR11599:SF14 PROTEASOME SUBUNIT ALPHA TYPE-5 108 343 7.5E-103
5 g5573.t1 PANTHER PTHR11599 PROTEASOME SUBUNIT ALPHA/BETA 108 343 7.5E-103
3 g5573.t1 Pfam PF07096 Protein of unknown function (DUF1358) 4 104 2.9E-33
2 g5573.t1 Pfam PF10584 Proteasome subunit A N-terminal signature 111 133 2.8E-12
1 g5573.t1 Pfam PF00227 Proteasome subunit 134 323 2.4E-53
8 g5573.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
12 g5573.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 40 -
10 g5573.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 41 68 -
11 g5573.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 69 89 -
9 g5573.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 90 345 -
16 g5573.t1 ProSitePatterns PS00388 Proteasome alpha-type subunits signature. 111 133 -
18 g5573.t1 ProSiteProfiles PS51475 Proteasome alpha-type subunit profile. 126 342 76.873
17 g5573.t1 SMART SM00948 Proteasome_A_N_2 111 133 1.5E-9
6 g5573.t1 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases) 110 342 2.24E-74
14 g5573.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 19 41 -
15 g5573.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 69 91 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5573/g5573.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5573.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0019773 proteasome core complex, alpha-subunit complex CC
GO:0051603 proteolysis involved in cellular protein catabolic process BP
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process BP
GO:0006511 ubiquitin-dependent protein catabolic process BP
GO:0005839 proteasome core complex CC

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