General information for g567.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g567 is located on chr_3: 4170778..4171803 (+ 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_3 | g567 | g567.t13 | isoform | g567.t13 | 4169872 | 4171502 |
| chr_3 | g567 | g567.t13 | exon | g567.t13.exon1 | 4169872 | 4170520 |
| chr_3 | g567 | g567.t13 | cds | g567.t13.CDS1 | 4170070 | 4170520 |
| chr_3 | g567 | g567.t13 | exon | g567.t13.exon2 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t13 | cds | g567.t13.CDS2 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t13 | exon | g567.t13.exon3 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t13 | cds | g567.t13.CDS3 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t13 | exon | g567.t13.exon4 | 4171103 | 4171221 |
| chr_3 | g567 | g567.t13 | cds | g567.t13.CDS4 | 4171103 | 4171135 |
| chr_3 | g567 | g567.t13 | exon | g567.t13.exon5 | 4171422 | 4171502 |
| chr_3 | g567 | g567.t13 | TTS | g567.t13 | 4171812 | 4171812 |
| chr_3 | g567 | g567.t13 | TSS | g567.t13 | NA | NA |
Sequences
>g567.t13 Gene=g567 Length=1217
AAAAATTTAGATGATGAAGAAATAGACTTGAGGCCATTAATCGACTATAATGGAAATTAT
TTGGCAAGAGTAAATGAAACAACCTTGCCAAATGAAACGTCAAAAAATAATGTGTCCTAC
TTGTTGAATGTATGTCGCCCGATAAATTCATTTTATTCATTAAATTGTCATGGAAATACT
GGCGCTTGTAGAACAATCATGAAAGATGAAAAACACGAAGAGGAAATAAGCTTAGGTCAC
TTTGAATATTTTATGTCTACTGAAAAGGGAAAAATTGAAGGTACAAACAATGTTATAATG
AAATATTTCCATGGATCAAAATGTCCAACTGATAAAGAGGAAGAGATAACAACGAAAGTT
AAATTCTATTGTGATGAGAATGCTGGTTTGGGAAGTCCTATTTTACAATCTATTGAGCAT
TGTGAATATTCATTTGAATTTCCAACCAGCATCTTATGCAATGATAAGCGTGTCAATCTG
AAAAGCAATGAATCGTGCATACTGACGAATGGTGATTCGAGTGTCAATTTGAAATCTTAT
GGAAATTTCAATACAAGCAACAGAAACATAAGTTTGTGTGATGCACTTGTGAAGACATAC
ACTATCAGCTATAAACAATCAATGGTTATTATTGAATATGTTGATAAAGATTACGTCGAT
ATAGAAGTTCAACTTAAATGTAATTTGAAAAATAATACATTTGTTGATGTTAGCAATGAG
GGTATCATCATTATGAATGAGTCACCTTTGATTTGTCCACTTTTGCATATCGTACCAAAA
GCTACACCATCACAGAATGAAGTTGATAACGATAACAATGATGTGCTAGAGATGTCATTA
AACAATGATATAATAATACCAAAATCAAGCAAATTTCCATTGGGTTATTTGTTCCTAATT
TCAATTTTGATTGCTGCATTTGGAATTTTCTATATTGTCATAAGAAATCCTGAGCGTCGC
GACATAATTCGCAATATGATTAAATTCCGATCTCGGTCAAATGTTCGATACACACGAAAC
ATGAATGATGACGATTTAATTTTAAACTAGTTATGCCAATATAGTTTTCTTTCCATTACA
CTTGTTATCATCCTAAAACAAAACAAAATAGTTCCTGTAGAAAAATCACTATGCATGTGC
GACTTAATGAAGAATCAGCCCTCTTAGATGGTAATAGTCCAAATTCAGATAGTGATGATG
AGAATATTTTGCTGTAA
>g567.t13 Gene=g567 Length=283
MKDEKHEEEISLGHFEYFMSTEKGKIEGTNNVIMKYFHGSKCPTDKEEEITTKVKFYCDE
NAGLGSPILQSIEHCEYSFEFPTSILCNDKRVNLKSNESCILTNGDSSVNLKSYGNFNTS
NRNISLCDALVKTYTISYKQSMVIIEYVDKDYVDIEVQLKCNLKNNTFVDVSNEGIIIMN
ESPLICPLLHIVPKATPSQNEVDNDNNDVLEMSLNNDIIIPKSSKFPLGYLFLISILIAA
FGIFYIVIRNPERRDIIRNMIKFRSRSNVRYTRNMNDDDLILN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g567.t13 | Gene3D | G3DSA:2.70.130.10 | - | 1 | 91 | 1.2E-14 |
| 1 | g567.t13 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 49 | 104 | 8.5E-5 |
| 7 | g567.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 227 | - |
| 8 | g567.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 228 | 248 | - |
| 6 | g567.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 249 | 283 | - |
| 4 | g567.t13 | SMART | SM01404 | CIMR_2 | 47 | 154 | 0.0087 |
| 3 | g567.t13 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 7 | 87 | 3.79E-13 |
| 2 | g567.t13 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 226 | 248 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g567/g567.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t13.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0038023 | signaling receptor activity | MF |
| GO:0007041 | lysosomal transport | BP |
| GO:0005537 | mannose binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
