General information for g5043.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peroxisomal membrane protein PEX13.
Parent gene
- The parent gene g5043 is located on chr_2: 6594368..6595766 (+ 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_2 | g5043 | g5043.t3 | TSS | g5043.t3 | 6594122 | 6594122 |
| chr_2 | g5043 | g5043.t3 | isoform | g5043.t3 | 6594368 | 6595766 |
| chr_2 | g5043 | g5043.t3 | exon | g5043.t3.exon1 | 6594368 | 6595328 |
| chr_2 | g5043 | g5043.t3 | cds | g5043.t3.CDS1 | 6594698 | 6595328 |
| chr_2 | g5043 | g5043.t3 | exon | g5043.t3.exon2 | 6595387 | 6595766 |
| chr_2 | g5043 | g5043.t3 | cds | g5043.t3.CDS2 | 6595387 | 6595766 |
| chr_2 | g5043 | g5043.t3 | TTS | g5043.t3 | 6595975 | 6595975 |
Sequences
>g5043.t3 Gene=g5043 Length=1341
ATGACTTTAGACTCAACAACGCTGCCCTTGGCAAATGGTTATGCACCTGTTAATTATCGA
CAACAAGTAAATATGGGCGGTAGTGATGTATTCGGTGGACCTTATCAAATTCAGACACCA
TCAGGTAGTTTTTTACTATAATATAATATGTCGCATTTAAACCTAATTCTTCTTATCAGA
AGTCTTATCTTATATTAATATTAACGACATCTCTGACACAATTTTAATTTATTTGTAGGC
ATTGTGCACTCAACACAGCCATCAGCACAAATTACACCTCCACCACTGCCGCCACGACCG
AATTCATATTTACAATCATCATCATCATCCATGTTTTCACCTTATGGCAATAATTATGGC
TTCAATTCATTTGGTGGTGGATTTAATTCGAATTATGGTTATGGCATGGGCGGATTCAAT
TCTTTTAATTCATTTGGAGGTTTTGGAAGTGGATACGGAAGACCATTTGGCAATCCATTA
GATCCAGAAATGAGATTTATACAAATGGCAGAAGAAAGTTCACGATCAACATTTCAAAGT
ATTGAGTCAGTTGTATCAACTATTGGAAATATTGCAACTATGCTTGATAGTACTTATTTT
GCATTAACAAGTTCATTCCGAGCAATATTGGGTCTTGCTGCAAACTTTTCACATCTTCGT
GGATTCTTTTCGAAATTCTTTTCAACATTTGCAGTGTTCAGAACTGCACTTTGGATGTAC
AAAAAATTTCTTTATATACTCGGCATATCAAAATTCAATCCATCAACACAAATGAATTTG
AATGAAGCATTTAAAGATGCTGAAGAAATGCAGCAATCATCAAATGATTTTTTCAATTCG
GCTGCATCACAACAGCAAGGTTCAGGATTAGCAATGGTTTTATTTTTAACATTTATATTT
ACTGCGCCATATTTAATTATGAAACTTTTTGGTTCGATAATGAACTCATCTGTTGACAAT
TCTAAAAATCCTTCTGCATGGGTAAATGCCATTGATGCTGTAGTAACCTACAACTTTAAT
GCAGATCATCCGTCAGAATTGTCTGTAAGAGCAGGACAAGTAATCAAAATTGCACCAAAG
GAAATTCAACAATTGAATAGACTTCTTTCGACAAATTGGCTTTTGGCAACAGCTGATGGC
AAAAATGTCGGCCTTGTACCTGTCAACTACATACGAAGGCAAACAGCAACGAATGAGTTT
GTTTATACTCAGCAGCAACAGCAACAACAGCAGCCGCTGCCATCTCAACAAACTCAAGAG
GCAACAATTGAGCAACAGTCTGATTTAGTAATGGAGCCTTTAATAATAAAAGACGAAAAT
TCCACAGAAAATCAAGTGTAA
>g5043.t3 Gene=g5043 Length=336
MFSPYGNNYGFNSFGGGFNSNYGYGMGGFNSFNSFGGFGSGYGRPFGNPLDPEMRFIQMA
EESSRSTFQSIESVVSTIGNIATMLDSTYFALTSSFRAILGLAANFSHLRGFFSKFFSTF
AVFRTALWMYKKFLYILGISKFNPSTQMNLNEAFKDAEEMQQSSNDFFNSAASQQQGSGL
AMVLFLTFIFTAPYLIMKLFGSIMNSSVDNSKNPSAWVNAIDAVVTYNFNADHPSELSVR
AGQVIKIAPKEIQQLNRLLSTNWLLATADGKNVGLVPVNYIRRQTATNEFVYTQQQQQQQ
QPLPSQQTQEATIEQQSDLVMEPLIIKDENSTENQV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5043.t3 | CDD | cd11864 | SH3_PEX13_eumet | 223 | 282 | 1.1423E-23 |
| 6 | g5043.t3 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 218 | 315 | 7.3E-12 |
| 13 | g5043.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 295 | 314 | - |
| 3 | g5043.t3 | PANTHER | PTHR19332 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 5 | 299 | 5.5E-58 |
| 4 | g5043.t3 | PANTHER | PTHR19332:SF1 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 5 | 299 | 5.5E-58 |
| 1 | g5043.t3 | Pfam | PF04088 | Peroxin 13, N-terminal region | 55 | 199 | 1.0E-36 |
| 2 | g5043.t3 | Pfam | PF07653 | Variant SH3 domain | 224 | 281 | 5.6E-5 |
| 8 | g5043.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 178 | - |
| 9 | g5043.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 197 | - |
| 7 | g5043.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 198 | 336 | - |
| 14 | g5043.t3 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 218 | 286 | 16.682 |
| 12 | g5043.t3 | SMART | SM00326 | SH3_2 | 221 | 285 | 1.5E-7 |
| 5 | g5043.t3 | SUPERFAMILY | SSF50044 | SH3-domain | 206 | 283 | 1.27E-10 |
| 11 | g5043.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 177 | 196 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5043/g5043.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5043.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
| GO:0016560 | protein import into peroxisome matrix, docking | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0005777 | peroxisome | CC |
KEGG
Orthology
- This transcript has been annotated with K13344 (peroxin-13)
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.
