Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Extracellular superoxide dismutase [Cu-Zn].

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 g13490 g13490.t5 isoform g13490.t5 30455899 30458342
chr_1 g13490 g13490.t5 exon g13490.t5.exon1 30455899 30457251
chr_1 g13490 g13490.t5 TTS g13490.t5 30455908 30455908
chr_1 g13490 g13490.t5 cds g13490.t5.CDS1 30457155 30457251
chr_1 g13490 g13490.t5 exon g13490.t5.exon2 30457522 30457818
chr_1 g13490 g13490.t5 cds g13490.t5.CDS2 30457522 30457818
chr_1 g13490 g13490.t5 exon g13490.t5.exon3 30457941 30458040
chr_1 g13490 g13490.t5 cds g13490.t5.CDS3 30457941 30458040
chr_1 g13490 g13490.t5 exon g13490.t5.exon4 30458178 30458342
chr_1 g13490 g13490.t5 cds g13490.t5.CDS4 30458178 30458295
chr_1 g13490 g13490.t5 TSS g13490.t5 NA NA

Sequences

>g13490.t5 Gene=g13490 Length=1915
ATCAGTTGCAATCATTTCATTCAACATCAAAGACCTAAAAATACGAGATGAAATCCTTAG
TCATCATTTTCGTAATTTGTCTCTCAACAATCATCGTCAATGGCGATGAAGCGAAGCCTG
CAAAAGCTATAGCAGTGCTTGGATTCTCAAACTCCGTCCATGGAAACATCACTTTCTCAC
AATCATCCTGTACGGAAGCAGTTCTCGTTCAAATTGAAATAACTGGCCTTACACCAGGCA
AACACGGCTTTCATGTTCACGAAAAATTTCTCACATATAGGAGCACAGGAAGTCATTTCA
ACCCAGATCGCTTGAATCATGGCGCACGTGAAGCACAAGTTCGTCACGTTGGTGATTTGG
GCAACGTTGTTGCTGATGATCAAGGACGCGTCTCAACATCATTTTCGGATAATGTCATTA
CATTGTTTGGTGCTCGAAGTATCATTGGTAGAGCAATTGTTGTTCACACCGATGAAGATG
ACCTTGGTCTTACCGATCATCAAGACTCTCATAAAACGGGAAATGCTGGTGGACGTGTTG
CATGCGGAATTATTGGAATCTTGGAGCCATCGAATGACGAATGGACATGTAATTCATCAT
CGAGAACACAAGTGGGATTATTGTTGATTCTCGTTATTATTGCTGTAATTAGAGCATAAA
CTCTTCTCTTTTATTTATTTGTAGCATACTCGCTAATTCTAATGTTCGTTGTTGCTGTTA
TTGTTTGTGAAATGGAATTAAAGACAACTCATACACACACTCTGACACACACAGTCTTGT
TGACCATTTGACACATTTTTATCATGAATATTCTTGTATTTGAATGAATATTTTGATTTA
TTAAAGTTGAAACTTGAAAACTCTTTTATACTCACAATTTTTATTGTTTATTTATTTCTT
GGTTTATATTTTTGATTTTTATAGACCTGATTATTTGTTTATTAATGAATTAAACTATAA
ACTCACTTTAAAACAATCTAAATAGTAAAATTCAAAAAAGCAGTTAAGATCAATTTTATT
CACAATAAATTAATTTTGAGTGTAAATTTTCGACTAAAATTTTTCGTCGAGATTTAAATT
ATTCGGTCAGATTAAAAATAAATCTTTCCAAAATAAATCGTAAGATTTGAGAATTAAATT
TTTTTAAGAAAAAAATAAAATTGGACATCAAAAGAGTTTTCAAGCTTTAAGTTTTGCAAA
AAATTCAGCATACTTTTCATTTTCCTTTTTTACATAAGATTGATGATGCTTCTCATAAGA
AATTGAAAATGCTCATAAAAATGTCCCTTTCATATTCTCCTTTTTCTGAATCTGTCGCTG
TCTGTGAATTAATTCACAAGAGAGATATGACCAAAATGGCATGACATTTCATAACCAAAA
AATCCCTGCATCCTTTGCCATATGTCCACTTACGCTTCATCTTTCTCATGTCACATCTGC
TTCTTTTTTTTAGTTTTTTTTCCAAATGTTTAGGAAATGTTTGATGGTTTTTTAAATTTT
TTTTACTTATTTAATAATCAATCATTGACAAACAATTACCTACTTTAGTTACATTCATAT
TTATTGCTTTGAAAGCACCTCATATAAATGAGATCAATATAAAATTTGGTTCCTCTTAAA
AGTGATTTACATAACGACATTTTCTCTCCTTCTCTTTTCTTTTTGTGGCCATCATTTTTC
TGTTGTGCTTATTCATGTATTTGTATGTATATTATAAATGGTAAACTACTCCAATGGCAC
AATCCCTCCCACACACATATAACGTTGAATCAGCAATAATGCTTCTCATAGTAATATTTG
AAATTGGTTTACGTAAAGTAAATTTCCTTCTCTCTTCCCTGGTGAGGTTTTCGAAGTAAA
AGAGAATATTTAGGGTTAAATAAAGATTTGCTATGTTAGAAAAAGGAATGAAACT

>g13490.t5 Gene=g13490 Length=203
MKSLVIIFVICLSTIIVNGDEAKPAKAIAVLGFSNSVHGNITFSQSSCTEAVLVQIEITG
LTPGKHGFHVHEKFLTYRSTGSHFNPDRLNHGAREAQVRHVGDLGNVVADDQGRVSTSFS
DNVITLFGARSIIGRAIVVHTDEDDLGLTDHQDSHKTGNAGGRVACGIIGILEPSNDEWT
CNSSSRTQVGLLLILVIIAVIRA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g13490.t5 CDD cd00305 Cu-Zn_Superoxide_Dismutase 26 166 7.94298E-51
11 g13490.t5 Gene3D G3DSA:2.60.40.200 - 22 180 3.1E-50
2 g13490.t5 PANTHER PTHR10003 SUPEROXIDE DISMUTASE CU-ZN -RELATED 12 173 5.7E-47
3 g13490.t5 PANTHER PTHR10003:SF31 SUPEROXIDE DISMUTASE [CU-ZN] 3 12 173 5.7E-47
7 g13490.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 64 86 1.9E-29
5 g13490.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 100 109 1.9E-29
4 g13490.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 119 141 1.9E-29
6 g13490.t5 PRINTS PR00068 Cu-Zn-superoxide dismutase family signature 144 170 1.9E-29
1 g13490.t5 Pfam PF00080 Copper/zinc superoxide dismutase (SODC) 34 169 1.3E-40
13 g13490.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
14 g13490.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
15 g13490.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
16 g13490.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 19 -
12 g13490.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 203 -
18 g13490.t5 ProSitePatterns PS00332 Copper/Zinc superoxide dismutase signature 2. 158 169 -
8 g13490.t5 SUPERFAMILY SSF49329 Cu,Zn superoxide dismutase-like 26 172 1.44E-46
10 g13490.t5 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
9 g13490.t5 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 22 -

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:0006801 superoxide metabolic process BP
GO:0004784 superoxide dismutase activity MF
GO:0046872 metal ion binding MF
GO:0055114 NA NA

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. There were no conditions that were differentially expressed