General information for g12929.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Peroxisome biogenesis factor 10.
Parent gene
- The parent gene g12929 is located on chr_1: 26975974..26976876 (- 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 | g12929 | g12929.t1 | TTS | g12929.t1 | 26975901 | 26975901 |
| chr_1 | g12929 | g12929.t1 | isoform | g12929.t1 | 26975974 | 26976876 |
| chr_1 | g12929 | g12929.t1 | exon | g12929.t1.exon1 | 26975974 | 26976876 |
| chr_1 | g12929 | g12929.t1 | cds | g12929.t1.CDS1 | 26975974 | 26976876 |
| chr_1 | g12929 | g12929.t1 | TSS | g12929.t1 | 26977720 | 26977720 |
Sequences
>g12929.t1 Gene=g12929 Length=903
ATGGTTAAAAGTTATATTAAAAAAGCAAGACAACCTGAAGTAATTCGAACAATACAAAAA
GACCTTCAATACACAACAGAACTCAATCAAGATGTGTTAGAGGTGACACAATTTTTAGCA
AAAAACAACCGTAATATAATAAAACTGAATGAATTTATCAAAGTATTTGTAAATGTTGCT
TATCATGGATTTGCGGCGATAAATAGATTGCAAACTTTAGGAGAAGAATACACAGGTGTA
ATACAAATTGATACTAAGACAGATAATTTACCTAAAAAATTTATTCAAGTGATTGCAATC
ATATTTGAATTTGGTGGCGAAGGTTTTTTAATTAAAGTGTTGAATGAGTATGAAAAGAAG
GTCAATGACAGCGAGGATTTACTTCCTGAAGCACGTAGAACGATTATTACAATAATTAGC
ATCTTAAAATCATCTATTCCATACATTAAAGCAATTCATCGTGGCATCTTTTATCTAAAT
AATTCAGGTCAATTGCAAATTTCCAAAGGACTAACGGGAATACATTATGTGCTAACACGC
TTTTGGTTGAATAACCATCACAATACAGGTGGTTATAAATTTCTTGGTATTGTGACACTT
TTGCAAGTAGTGTTTTCACTCTTACTGAAATTGAAAGAGAAACATGAAGAAAAAAAATTG
CGAAAAATTGAGAGAGAAACAAGAGAAAGTACGCAATCAAGGTTGCAGCTTCAATTACCC
AACGAAGATACAAAAAAGTGTATTTTATGCTTGGAAGGCCGTATAAATTTGACTTCAACT
TCATGTGGTCATCTTTATTGTTGGAACTGTATTTGTGATTGGCTAAAATATAAAAGTGAA
TGCCCAATATGTCGTGAGCATTTAACACAAAGTTCTGTGATATTTTTACAGAATTATTAT
TAA
>g12929.t1 Gene=g12929 Length=300
MVKSYIKKARQPEVIRTIQKDLQYTTELNQDVLEVTQFLAKNNRNIIKLNEFIKVFVNVA
YHGFAAINRLQTLGEEYTGVIQIDTKTDNLPKKFIQVIAIIFEFGGEGFLIKVLNEYEKK
VNDSEDLLPEARRTIITIISILKSSIPYIKAIHRGIFYLNNSGQLQISKGLTGIHYVLTR
FWLNNHHNTGGYKFLGIVTLLQVVFSLLLKLKEKHEEKKLRKIERETRESTQSRLQLQLP
NEDTKKCILCLEGRINLTSTSCGHLYCWNCICDWLKYKSECPICREHLTQSSVIFLQNYY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g12929.t1 | CDD | cd16527 | RING-HC_PEX10 | 246 | 285 | 4.39697E-20 |
| 7 | g12929.t1 | Coils | Coil | Coil | 114 | 134 | - |
| 6 | g12929.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 210 | 300 | 1.9E-14 |
| 3 | g12929.t1 | PANTHER | PTHR23350 | PEROXISOME ASSEMBLY PROTEIN 10 | 5 | 297 | 2.6E-50 |
| 4 | g12929.t1 | PANTHER | PTHR23350:SF0 | PEROXISOME BIOGENESIS FACTOR 10 | 5 | 297 | 2.6E-50 |
| 1 | g12929.t1 | Pfam | PF04757 | Pex2 / Pex12 amino terminal region | 34 | 213 | 7.6E-10 |
| 2 | g12929.t1 | Pfam | PF13920 | Zinc finger, C3HC4 type (RING finger) | 245 | 290 | 1.0E-8 |
| 8 | g12929.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 93 | - |
| 11 | g12929.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 94 | 114 | - |
| 10 | g12929.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 115 | 190 | - |
| 12 | g12929.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 191 | 211 | - |
| 9 | g12929.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 212 | 300 | - |
| 15 | g12929.t1 | ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 262 | 271 | - |
| 16 | g12929.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 247 | 285 | 11.855 |
| 14 | g12929.t1 | SMART | SM00184 | ring_2 | 247 | 284 | 8.1E-6 |
| 5 | g12929.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 235 | 291 | 1.37E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K13346 (peroxin-10)
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.
