General information for g5043.t1
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.t1 | TSS | g5043.t1 | 6594122 | 6594122 |
| chr_2 | g5043 | g5043.t1 | isoform | g5043.t1 | 6594368 | 6595766 |
| chr_2 | g5043 | g5043.t1 | exon | g5043.t1.exon1 | 6594368 | 6594491 |
| chr_2 | g5043 | g5043.t1 | cds | g5043.t1.CDS1 | 6594368 | 6594491 |
| chr_2 | g5043 | g5043.t1 | exon | g5043.t1.exon2 | 6594606 | 6595328 |
| chr_2 | g5043 | g5043.t1 | cds | g5043.t1.CDS2 | 6594606 | 6595328 |
| chr_2 | g5043 | g5043.t1 | exon | g5043.t1.exon3 | 6595387 | 6595766 |
| chr_2 | g5043 | g5043.t1 | cds | g5043.t1.CDS3 | 6595387 | 6595766 |
| chr_2 | g5043 | g5043.t1 | TTS | g5043.t1 | 6595975 | 6595975 |
Sequences
>g5043.t1 Gene=g5043 Length=1227
ATGACTTTAGACTCAACAACGCTGCCCTTGGCAAATGGTTATGCACCTGTTAATTATCGA
CAACAAGTAAATATGGGCGGTAGTGATGTATTCGGTGGACCTTATCAAATTCAGACACCA
TCAGGCATTGTGCACTCAACACAGCCATCAGCACAAATTACACCTCCACCACTGCCGCCA
CGACCGAATTCATATTTACAATCATCATCATCATCCATGTTTTCACCTTATGGCAATAAT
TATGGCTTCAATTCATTTGGTGGTGGATTTAATTCGAATTATGGTTATGGCATGGGCGGA
TTCAATTCTTTTAATTCATTTGGAGGTTTTGGAAGTGGATACGGAAGACCATTTGGCAAT
CCATTAGATCCAGAAATGAGATTTATACAAATGGCAGAAGAAAGTTCACGATCAACATTT
CAAAGTATTGAGTCAGTTGTATCAACTATTGGAAATATTGCAACTATGCTTGATAGTACT
TATTTTGCATTAACAAGTTCATTCCGAGCAATATTGGGTCTTGCTGCAAACTTTTCACAT
CTTCGTGGATTCTTTTCGAAATTCTTTTCAACATTTGCAGTGTTCAGAACTGCACTTTGG
ATGTACAAAAAATTTCTTTATATACTCGGCATATCAAAATTCAATCCATCAACACAAATG
AATTTGAATGAAGCATTTAAAGATGCTGAAGAAATGCAGCAATCATCAAATGATTTTTTC
AATTCGGCTGCATCACAACAGCAAGGTTCAGGATTAGCAATGGTTTTATTTTTAACATTT
ATATTTACTGCGCCATATTTAATTATGAAACTTTTTGGTTCGATAATGAACTCATCTGTT
GACAATTCTAAAAATCCTTCTGCATGGGTAAATGCCATTGATGCTGTAGTAACCTACAAC
TTTAATGCAGATCATCCGTCAGAATTGTCTGTAAGAGCAGGACAAGTAATCAAAATTGCA
CCAAAGGAAATTCAACAATTGAATAGACTTCTTTCGACAAATTGGCTTTTGGCAACAGCT
GATGGCAAAAATGTCGGCCTTGTACCTGTCAACTACATACGAAGGCAAACAGCAACGAAT
GAGTTTGTTTATACTCAGCAGCAACAGCAACAACAGCAGCCGCTGCCATCTCAACAAACT
CAAGAGGCAACAATTGAGCAACAGTCTGATTTAGTAATGGAGCCTTTAATAATAAAAGAC
GAAAATTCCACAGAAAATCAAGTGTAA
>g5043.t1 Gene=g5043 Length=408
MTLDSTTLPLANGYAPVNYRQQVNMGGSDVFGGPYQIQTPSGIVHSTQPSAQITPPPLPP
RPNSYLQSSSSSMFSPYGNNYGFNSFGGGFNSNYGYGMGGFNSFNSFGGFGSGYGRPFGN
PLDPEMRFIQMAEESSRSTFQSIESVVSTIGNIATMLDSTYFALTSSFRAILGLAANFSH
LRGFFSKFFSTFAVFRTALWMYKKFLYILGISKFNPSTQMNLNEAFKDAEEMQQSSNDFF
NSAASQQQGSGLAMVLFLTFIFTAPYLIMKLFGSIMNSSVDNSKNPSAWVNAIDAVVTYN
FNADHPSELSVRAGQVIKIAPKEIQQLNRLLSTNWLLATADGKNVGLVPVNYIRRQTATN
EFVYTQQQQQQQQPLPSQQTQEATIEQQSDLVMEPLIIKDENSTENQV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5043.t1 | CDD | cd11864 | SH3_PEX13_eumet | 295 | 354 | 3.31682E-23 |
| 6 | g5043.t1 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 290 | 387 | 1.0E-11 |
| 14 | g5043.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 367 | 386 | - |
| 3 | g5043.t1 | PANTHER | PTHR19332 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 42 | 371 | 9.3E-64 |
| 4 | g5043.t1 | PANTHER | PTHR19332:SF1 | PEROXISOMAL MEMBRANE PROTEIN PEX13 | 42 | 371 | 9.3E-64 |
| 1 | g5043.t1 | Pfam | PF04088 | Peroxin 13, N-terminal region | 127 | 271 | 1.6E-36 |
| 2 | g5043.t1 | Pfam | PF07653 | Variant SH3 domain | 296 | 353 | 7.5E-5 |
| 8 | g5043.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 250 | - |
| 9 | g5043.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 269 | - |
| 7 | g5043.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 270 | 408 | - |
| 15 | g5043.t1 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 290 | 358 | 16.682 |
| 13 | g5043.t1 | SMART | SM00326 | SH3_2 | 293 | 357 | 1.5E-7 |
| 5 | g5043.t1 | SUPERFAMILY | SSF50044 | SH3-domain | 278 | 355 | 1.71E-10 |
| 11 | g5043.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 210 | - |
| 12 | g5043.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 268 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5043/g5043.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5043.t1.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.
