General information for g567.t4
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.t4 | TSS | g567.t4 | 4167939 | 4167939 |
| chr_3 | g567 | g567.t4 | isoform | g567.t4 | 4168099 | 4169428 |
| chr_3 | g567 | g567.t4 | exon | g567.t4.exon1 | 4168099 | 4168676 |
| chr_3 | g567 | g567.t4 | exon | g567.t4.exon2 | 4168807 | 4169428 |
| chr_3 | g567 | g567.t4 | cds | g567.t4.CDS1 | 4168969 | 4169427 |
| chr_3 | g567 | g567.t4 | TTS | g567.t4 | NA | NA |
Sequences
>g567.t4 Gene=g567 Length=1200
ATGAAGTATTTCGCAATTTTCCTGCTTGTGATAAATTTCTGCAATATAATTGCAATAGAT
CAAACAGTATGTATGAATAAAACCTTGAATTACCAACTTTCTAGAATAAATTTTTTAAAT
TTAATTTAATTTGATTAATGTCATCAAAAAATACCATCATTTCCCCGAACAAAGAAGTTC
TTATCTTATTAATCACTCTCTATTCGTCATCATGATATTTAGTCTTTATCGTTCGCTTTT
TTTCGTGATTATTTATTTACGTTCTTTTCTTTTCTTTCTTGCACCTATTTGTGTACAAAA
ATATAACATCATCTTTAATATATTTATTGTGTGCATTGACCTGTATTGACGAAAATAGAA
AGACGTTGAAGGAGCAAATTGTTCAGTGACAGAGACAATTGGAAATTATACATTTAATTT
TACTGAACTTAGTAGTGACTTTGGATATCACATCGATGGAAATGCAGAAGATATGGGAAA
ATATAGTTTCAATCTTTGTAAACCGCTATCAAGAAAATGCAACAACCAAACAGCTGCAGC
TTGTCTGAAAAATGTTGACGGCAAGGAAATCATAATAGTTTTGGAATGACGGTCAAATAA
GATTCAGTTTCATTGGCGAAAAGTGTAATAAACTTGAAAACTATACTTTAAATGTGATAC
TTCAATGCGATTATGCTGAAACGAAAAATGATTTTCTTGGCGTGTTTCATGATGATAGCG
AATGTGAAGTTACAATACTTATGCGAACGCCAAAGGCGTGTTTAGAAATTCCTGAAAATG
TCAAAAATGCAAAGATGTACGTAACTAGTCCCAATGGCAAGATTTTGAATTTCAACGCTT
TAAAAAGTTCAAACCATATTATCAATGGTCCAAATGATGGAACTTTCATAATTGGTTTTC
CAATTACTTACGAACATGGAATTTTATGTGAAGCTGGCTCATCTATTTGTTATGTCGACA
AGAATGAGACTGATTTATCAAAGAAATATACCAATATGGGAACGATGACATCTAATATTG
AATTTGAAAATGATCGACCAGTCATTAAATTTACAAGCAAAGAAAAATGCAATAATAACA
CATTGGGCTCATCAAAAATTGTTTTCGAATGTGATCGATTCAAAAAAGAAGGTACACCTA
AATTTAAAGGTGTAAAAGATTGTGTAAGCAATTTTGTTTGGGAAACATCACTTGCATGTT
>g567.t4 Gene=g567 Length=153
MRTPKACLEIPENVKNAKMYVTSPNGKILNFNALKSSNHIINGPNDGTFIIGFPITYEHG
ILCEAGSSICYVDKNETDLSKKYTNMGTMTSNIEFENDRPVIKFTSKEKCNNNTLGSSKI
VFECDRFKKEGTPKFKGVKDCVSNFVWETSLAC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g567.t4 | Gene3D | G3DSA:2.70.130.10 | - | 14 | 153 | 0.0e+00 |
| 1 | g567.t4 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 118 | 153 | 7.4e-05 |
| 2 | g567.t4 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 18 | 153 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g567/g567.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t4.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.
