General information for g4172.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4172 is located on chr_3: 31195868..31197019 (- 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 | g4172 | g4172.t1 | isoform | g4172.t1 | 31195868 | 31197019 |
| chr_3 | g4172 | g4172.t1 | exon | g4172.t1.exon1 | 31195868 | 31196192 |
| chr_3 | g4172 | g4172.t1 | cds | g4172.t1.CDS1 | 31195868 | 31196192 |
| chr_3 | g4172 | g4172.t1 | exon | g4172.t1.exon2 | 31196415 | 31197019 |
| chr_3 | g4172 | g4172.t1 | cds | g4172.t1.CDS2 | 31196415 | 31197019 |
| chr_3 | g4172 | g4172.t1 | TSS | g4172.t1 | NA | NA |
| chr_3 | g4172 | g4172.t1 | TTS | g4172.t1 | NA | NA |
Sequences
>g4172.t1 Gene=g4172 Length=930
ATGCGTCAAATGTTTCGATGGATTTTGGAAGTGATTCAGTCAAAAAAAGATGATAAGACA
TCAAAAATTAAACCAATCATTGTGGATAGTGGAATAGCAGCTATCAGAAATTTCATTCAA
AATTTGAAACTCAAGAAAAAACCAATGCTCAGGATTTCTGGTAAAAAAACACAAATTTTC
TGTGAAACAATTGAAAGCAAAAAAATCATTTTGGACAAGCTCAAAATTCAGCAGTATAGA
TTTCATACATTCACGGAGGAATCGGAAAAATCAAAGATTTTCTTATTGAAGGGCTTTTAT
TTAGAGAAAGTTGAAAATGTCAAGAATTATCTGGTTAATGCTGGATTGAAAGTAAAGTCA
GTGAAGATATTTATTAATCATGAAGATTCTCCGATTATTGGTGTACAAATTGAAGAGAAA
ACTTCAATTAATGCGCTCAACCATTGCTATAAAAATATAGATTCAATATTCGTAAGATGG
GAAGTTCTTGATCGTAGCAAGAAAAAACTGACACAGTGCTATAATTGTCAACAATGGGGT
CACTCCTCAAACAATTGTGGCTATAAATCAAGATTGTGTGAAATGCCGAGAGTCACATGC
TCCTGTCTGAGTGAGAATTTCAGACCTAGTATTAATAATCAGACATTTGATCAACATGTA
ACATCTCCAACTATCAGTTCAACTCAAGATGTAGAAAAGGCCAATTCATTATTACAAAAA
TTCAATGAAGCTTGTAAGAAATTGAATGAAATTCCTGATGTAGAACAAACAATAAACAAC
TTTATTGACATGGTAAATAAACTTGCTGAAGCCAAAACCGAAACGGATAGGCAAATGATC
CTGGTTAGACATTTCAATATTCACAAGATAGATCTATCAAATGAAGCGATTCAACGAATT
AGCCTCGCATTCAAAAAATTTCCATCTTAG
>g4172.t1 Gene=g4172 Length=309
MRQMFRWILEVIQSKKDDKTSKIKPIIVDSGIAAIRNFIQNLKLKKKPMLRISGKKTQIF
CETIESKKIILDKLKIQQYRFHTFTEESEKSKIFLLKGFYLEKVENVKNYLVNAGLKVKS
VKIFINHEDSPIIGVQIEEKTSINALNHCYKNIDSIFVRWEVLDRSKKKLTQCYNCQQWG
HSSNNCGYKSRLCEMPRVTCSCLSENFRPSINNQTFDQHVTSPTISSTQDVEKANSLLQK
FNEACKKLNEIPDVEQTINNFIDMVNKLAEAKTETDRQMILVRHFNIHKIDLSNEAIQRI
SLAFKKFPS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g4172.t1 | Coils | Coil | Coil | 231 | 251 | - |
| g4172.t1 | ProSiteProfiles | PS50158 | Zinc finger CCHC-type profile. | 173 | 186 | 8.746 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid 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.
