General information for g13490.t178
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Extracellular superoxide dismutase [Cu-Zn].
Parent gene
- The parent gene g13490 is located on chr_1: 30457945..30461971 (- strand)
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.t178 | TTS | g13490.t178 | 30456939 | 30456939 |
| chr_1 | g13490 | g13490.t178 | isoform | g13490.t178 | 30457118 | 30461211 |
| chr_1 | g13490 | g13490.t178 | exon | g13490.t178.exon1 | 30457118 | 30457821 |
| chr_1 | g13490 | g13490.t178 | cds | g13490.t178.CDS1 | 30457518 | 30457821 |
| chr_1 | g13490 | g13490.t178 | exon | g13490.t178.exon2 | 30457941 | 30458040 |
| chr_1 | g13490 | g13490.t178 | cds | g13490.t178.CDS2 | 30457941 | 30458040 |
| chr_1 | g13490 | g13490.t178 | exon | g13490.t178.exon3 | 30458178 | 30458342 |
| chr_1 | g13490 | g13490.t178 | cds | g13490.t178.CDS3 | 30458178 | 30458295 |
| chr_1 | g13490 | g13490.t178 | exon | g13490.t178.exon4 | 30460580 | 30460782 |
| chr_1 | g13490 | g13490.t178 | exon | g13490.t178.exon5 | 30461015 | 30461211 |
| chr_1 | g13490 | g13490.t178 | TSS | g13490.t178 | 30461850 | 30461850 |
Sequences
>g13490.t178 Gene=g13490 Length=1369
CATTTACGCGCTTTGTTGATAAGTTGAGAGTTATTGGTTGCTTTTTCTATTATCAAATTT
AAACGTGCTAAAATTTCAAGTTAGATAATTATTTTCAAGTACTATTTGAGGCTTAAATAA
TAATTACTTTCTAATTTTGACTTCTATTTTCAAAGATAAGATAACAAAAACATGTTAATT
TATTTACATTCATGTTAGAATGCACTCGAGATTTGCTAATTAAAAAGAAAAACAAACAAT
AACATTCAGCAATAGCATCCCACGGAAAAAAACCCATCAAACAAGAAAGATTTGCGCACG
TTACTAAAGTTGTTTTTCTTCTTCTGTGTAATTACACTGAAGTTCTTGTTTCATAACAAT
ATTTTTTTTGTCGTATTTCAGTTTTGCGACAGAAGTTAAAATCAGTTGCAATCATTTCAT
TCAACATCAAAGACCTAAAAATACGAGATGAAATCCTTAGTCATCATTTTCGTAATTTGT
CTCTCAACAATCATCGTCAATGGCGATGAAGCGAAGCCTGCAAAAGCTATAGCAGTGCTT
GGATTCTCAAACTCCGTCCATGGAAACATCACTTTCTCACAATCATCCTGTACGGAAGCA
GTTCTCGTTCAAATTGAAATAACTGGCCTTACACCAGGCAAACACGGCTTTCATGTTCAC
GAAAACTTATTTCTCACATATAGGAGCACAGGAAGTCATTTCAACCCAGATCGCTTGAAT
CATGGCGCACGTGAAGCACAAGTTCGTCACGTTGGTGATTTGGGCAACGTTGTTGCTGAT
GATCAAGGACGCGTCTCAACATCATTTTCGGATAATGTCATTACATTGTTTGGTGCTCGA
AGTATCATTGGTAGAGCAATTGTTGTTCACACCGATGAAGATGACCTTGGTCTTACCGAT
CATCAAGACTCTCATAAAACGGGAAATGCTGGTGGACGTGTTGCATGCGGAATTATTGGA
ATCTTGTAAATATTTTTTTCTCTTTTCTCACTTTTCTTATCATCATTTTTGCTTTTTATA
CATACACAAGAATAAGAAGAGAATTTCTGTTTAGTGAGAATAAAAATAATTCTTAATCGT
CATGTGTTCATTTGACCCTGTAAAAATGTTATTAACTGTTGATGTGTGCGTGAGTAAAAT
GTATCAAGGTGAAGGTCATTTGCTCACACAATTGATAGCTAAATGTGCATTTATCACTTG
ACTTTTTTGATCGAATGAATTTCAATCATTTACAGGGAGCCATCGAATGACGAATGGACA
TGTAATTCATCATCGAGAACACAAGTGGGATTATTGTTGATTCTCGTTATTATTGCTGTA
ATTAGAGCATAAACTCTTCTCTTTTATTTATTTGTAGCATACTCGCTAA
>g13490.t178 Gene=g13490 Length=173
MKSLVIIFVICLSTIIVNGDEAKPAKAIAVLGFSNSVHGNITFSQSSCTEAVLVQIEITG
LTPGKHGFHVHENLFLTYRSTGSHFNPDRLNHGAREAQVRHVGDLGNVVADDQGRVSTSF
SDNVITLFGARSIIGRAIVVHTDEDDLGLTDHQDSHKTGNAGGRVACGIIGIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g13490.t178 | CDD | cd00305 | Cu-Zn_Superoxide_Dismutase | 26 | 167 | 4.66906E-49 |
| 11 | g13490.t178 | Gene3D | G3DSA:2.60.40.200 | - | 16 | 172 | 6.4E-51 |
| 2 | g13490.t178 | PANTHER | PTHR10003 | SUPEROXIDE DISMUTASE CU-ZN -RELATED | 12 | 172 | 4.0E-46 |
| 3 | g13490.t178 | PANTHER | PTHR10003:SF31 | SUPEROXIDE DISMUTASE [CU-ZN] 3 | 12 | 172 | 4.0E-46 |
| 5 | g13490.t178 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 65 | 87 | 1.1E-28 |
| 7 | g13490.t178 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 101 | 110 | 1.1E-28 |
| 6 | g13490.t178 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 120 | 142 | 1.1E-28 |
| 4 | g13490.t178 | PRINTS | PR00068 | Cu-Zn-superoxide dismutase family signature | 145 | 171 | 1.1E-28 |
| 1 | g13490.t178 | Pfam | PF00080 | Copper/zinc superoxide dismutase (SODC) | 34 | 170 | 1.5E-41 |
| 13 | g13490.t178 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 14 | g13490.t178 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g13490.t178 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 16 | g13490.t178 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 12 | g13490.t178 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 173 | - |
| 18 | g13490.t178 | ProSitePatterns | PS00332 | Copper/Zinc superoxide dismutase signature 2. | 159 | 170 | - |
| 8 | g13490.t178 | SUPERFAMILY | SSF49329 | Cu,Zn superoxide dismutase-like | 26 | 172 | 9.55E-47 |
| 10 | g13490.t178 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 9 | g13490.t178 | 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
- This transcript has been annotated with K04565 (superoxide dismutase, Cu-Zn family)
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