General information for g567.t5
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.t5 | TSS | g567.t5 | 4167939 | 4167939 |
| chr_3 | g567 | g567.t5 | isoform | g567.t5 | 4168099 | 4169724 |
| chr_3 | g567 | g567.t5 | exon | g567.t5.exon1 | 4168099 | 4168164 |
| chr_3 | g567 | g567.t5 | cds | g567.t5.CDS1 | 4168099 | 4168164 |
| chr_3 | g567 | g567.t5 | exon | g567.t5.exon2 | 4168457 | 4168676 |
| chr_3 | g567 | g567.t5 | cds | g567.t5.CDS2 | 4168457 | 4168676 |
| chr_3 | g567 | g567.t5 | exon | g567.t5.exon3 | 4168784 | 4169268 |
| chr_3 | g567 | g567.t5 | cds | g567.t5.CDS3 | 4168784 | 4169268 |
| chr_3 | g567 | g567.t5 | exon | g567.t5.exon4 | 4169615 | 4169724 |
| chr_3 | g567 | g567.t5 | cds | g567.t5.CDS4 | 4169615 | 4169641 |
| chr_3 | g567 | g567.t5 | TTS | g567.t5 | NA | NA |
Sequences
>g567.t5 Gene=g567 Length=881
ATGAAGTATTTCGCAATTTTCCTGCTTGTGATAAATTTCTGCAATATAATTGCAATAGAT
CAAACAAAAGACGTTGAAGGAGCAAATTGTTCAGTGACAGAGACAATTGGAAATTATACA
TTTAATTTTACTGAACTTAGTAGTGACTTTGGATATCACATCGATGGAAATGCAGAAGAT
ATGGGAAAATATAGTTTCAATCTTTGTAAACCGCTATCAAGAAAATGCAACAACCAAACA
GCTGCAGCTTGTCTGAAAAATGTTGACGGCAAGGAAATCATAATAGGATACGACAGCACT
TCAAAATTATTTTGGAATGACGGTCAAATAAGATTCAGTTTCATTGGCGAAAAGTGTAAT
AAACTTGAAAACTATACTTTAAATGTGATACTTCAATGCGATTATGCTGAAACGAAAAAT
GATTTTCTTGGCGTGTTTCATGATGATAGCGAATGTGAAGTTACAATACTTATGCGAACG
CCAAAGGCGTGTTTAGAAATTCCTGAAAATGTCAAAAATGCAAAGATGTACGTAACTAGT
CCCAATGGCAAGATTTTGAATTTCAACGCTTTAAAAAGTTCAAACCATATTATCAATGGT
CCAAATGATGGAACTTTCATAATTGGTTTTCCAATTACTTACGAACATGGAATTTTATGT
GAAGCTGGCTCATCTATTTGTTATGTCGACAAGAATGAGACTGATTTATCAAAGAAATAT
ACCAATATGGGAACGATGACATCTAATATTGAATTTGAAAATGATCGACCAGTGGCAATA
AACAAACAACAAAAGTAGGCATCTTCAATGCAAAACTTCAAGTCGAGAAGAAAAATGTAT
TTTTGAAATATGATGAAGGTTCTCAATGTGGTGATCCGAAA
>g567.t5 Gene=g567 Length=265
MKYFAIFLLVINFCNIIAIDQTKDVEGANCSVTETIGNYTFNFTELSSDFGYHIDGNAED
MGKYSFNLCKPLSRKCNNQTAAACLKNVDGKEIIIGYDSTSKLFWNDGQIRFSFIGEKCN
KLENYTLNVILQCDYAETKNDFLGVFHDDSECEVTILMRTPKACLEIPENVKNAKMYVTS
PNGKILNFNALKSSNHIINGPNDGTFIIGFPITYEHGILCEAGSSICYVDKNETDLSKKY
TNMGTMTSNIEFENDRPVAINKQQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g567.t5 | Gene3D | G3DSA:2.70.130.10 | - | 23 | 175 | 4.1E-21 |
| 6 | g567.t5 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 7 | g567.t5 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 8 | g567.t5 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 9 | g567.t5 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 5 | g567.t5 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 265 | - |
| 2 | g567.t5 | SMART | SM01404 | CIMR_2 | 3 | 120 | 0.0033 |
| 1 | g567.t5 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 25 | 164 | 2.22E-15 |
| 3 | g567.t5 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g567/g567.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t5.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
