General information for g12474.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12474 is located on chr_1: 23944195..23944981 (+ 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 | g12474 | g12474.t1 | TSS | g12474.t1 | 23944110 | 23944110 |
| chr_1 | g12474 | g12474.t1 | isoform | g12474.t1 | 23944195 | 23944981 |
| chr_1 | g12474 | g12474.t1 | exon | g12474.t1.exon1 | 23944195 | 23944198 |
| chr_1 | g12474 | g12474.t1 | cds | g12474.t1.CDS1 | 23944195 | 23944198 |
| chr_1 | g12474 | g12474.t1 | exon | g12474.t1.exon2 | 23944280 | 23944378 |
| chr_1 | g12474 | g12474.t1 | cds | g12474.t1.CDS2 | 23944280 | 23944378 |
| chr_1 | g12474 | g12474.t1 | exon | g12474.t1.exon3 | 23944591 | 23944810 |
| chr_1 | g12474 | g12474.t1 | cds | g12474.t1.CDS3 | 23944591 | 23944810 |
| chr_1 | g12474 | g12474.t1 | exon | g12474.t1.exon4 | 23944936 | 23944981 |
| chr_1 | g12474 | g12474.t1 | cds | g12474.t1.CDS4 | 23944936 | 23944981 |
| chr_1 | g12474 | g12474.t1 | TTS | g12474.t1 | 23945303 | 23945303 |
Sequences
>g12474.t1 Gene=g12474 Length=369
ATGGCATTAAATTGTACAACTTTAAGTCAAATTGACGACTCTCAACCACCACCATATAGT
AATTTGGCACAAACAATTCCAGCAGATGTAGTTCATAAACCAGCACACACAACAACAGTT
GTTGTACAACAAATTCATCCACCAACTTATGGCCCAAAACCTCAGTATGTGATGTGTTCT
TCATGCAAATCAATGACAATGACTAAAGTTAAGGACAAAGTGTCAATACGCACGCATAAA
ATGGCAATAATACTTGCTCTACTTAGCTGTTGCTCTTGTCTCTTGATTCCATACTGTCTC
TCGTCCTGCCAGAATCAACAACACGATTGTGAAAATTGCGGAGCATATCTGGGTACTTTT
AAAAACTGA
>g12474.t1 Gene=g12474 Length=122
MALNCTTLSQIDDSQPPPYSNLAQTIPADVVHKPAHTTTVVVQQIHPPTYGPKPQYVMCS
SCKSMTMTKVKDKVSIRTHKMAIILALLSCCSCLLIPYCLSSCQNQQHDCENCGAYLGTF
KN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12474.t1 | PANTHER | PTHR23292:SF14 | FI16615P1-RELATED | 23 | 122 | 4.9E-24 |
| 3 | g12474.t1 | PANTHER | PTHR23292 | LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR | 23 | 122 | 4.9E-24 |
| 1 | g12474.t1 | Pfam | PF10601 | LITAF-like zinc ribbon domain | 53 | 120 | 2.0E-18 |
| 6 | g12474.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 80 | - |
| 8 | g12474.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 98 | - |
| 7 | g12474.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 99 | 122 | - |
| 5 | g12474.t1 | ProSiteProfiles | PS51837 | LITAF domain profile. | 37 | 122 | 16.255 |
| 4 | g12474.t1 | SMART | SM00714 | litaf | 54 | 122 | 6.4E-12 |
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 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. There were no conditions that were differentially expressed