General information for g1978.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1978 is located on chr_3: 14175617..14176064 (+ 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 | g1978 | g1978.t2 | isoform | g1978.t2 | 14167742 | 14170572 |
| chr_3 | g1978 | g1978.t2 | exon | g1978.t2.exon1 | 14167742 | 14168281 |
| chr_3 | g1978 | g1978.t2 | cds | g1978.t2.CDS1 | 14168070 | 14168281 |
| chr_3 | g1978 | g1978.t2 | exon | g1978.t2.exon2 | 14168342 | 14168606 |
| chr_3 | g1978 | g1978.t2 | cds | g1978.t2.CDS2 | 14168342 | 14168597 |
| chr_3 | g1978 | g1978.t2 | exon | g1978.t2.exon3 | 14168670 | 14168841 |
| chr_3 | g1978 | g1978.t2 | exon | g1978.t2.exon4 | 14170282 | 14170572 |
| chr_3 | g1978 | g1978.t2 | TSS | g1978.t2 | NA | NA |
| chr_3 | g1978 | g1978.t2 | TTS | g1978.t2 | NA | NA |
Sequences
>g1978.t2 Gene=g1978 Length=1268
TTAATAAAGTTTTATAAGTTCATCACTAACAGCAGAAGGTGTCAAAATTCCAAGATCAGT
AAATATGAGAGTTATAAAGAGTGGAGGTGTAAAGTCAACTAACGGATGAATATTTGCCTT
TTCGCCATTTCTGTTTTGTATAAATTTATAAGTACTCGGTATATCTCGTTGATTGAGTGG
ATAAATTCGAGAGAATTTGAAACTTTCAGTTAAGACGTAAAATGGTTTGTTCATTTCACT
GGCACACAATGCAGCAGTAAAGGTTCCTATTCTATTTATTATCCCACCATTTTCCATTAC
GCCTTCTGCACCAGAAAAAACAAAGTCAATGCTTTCCATTGTGTATCCAATTGCAGCATC
AAGCACTAATGAAGCATCAATGTTTAATTGCTTTAAATCCTGTACCATCATCTCTCCCTC
ATTTTCATTTTTAAAGGAACTCATGCTCATTGTAACATATACTCGAAAATGTTTGTTCTT
TGAGGCAGCTAGTTTTAATGCTTCATACACTACTCTTGATCGACCTATTGTCAAGATTCT
ACATCCATCTGTAATAAAGTCTACAGAATTTTTAGCAATAACTTCACGACTGGCCAGCAG
TTTTCTTAAGAAACTTTGTCCTCTATTAGTCATTATTTTCTTTACTTCTTCCATGTCATA
CATTTCATCAATTTTTGGACTTGAGATAGTGATGAAGCACATGAAAAGTTCACATGAAGA
ACTAATTGATGTTATTGGTTTTCCACTTTCTTTTATTACTTTAATTGCAGATTTTATTGT
ATTAATCAACTCTTGAATTGTCACAAAGTTGTTTTCTCGAGAACCATAAGTAAAGTTTTA
ATTGCTGCTATTCCATACGACATATTATTGTCGTTATTAACGATATTAAGAAAATATCTT
TCGATTTGAGCATTATCCATGATAATATACAAATGAAATATAATTTTTAATGTTCCTGAT
GAAATTCAAAATAAACAAACATTTTTCGCAATTTGTCAGTCGCGTATAGTTATTTGATCT
GTGAGCACATTGTGGAAGCGGAGTAGGTTGTTTTAAATATGGCATCATCAACGCTAAATG
GAGAAATCAATAATATAAACTACACAGATGATGTTATTTCCCGTAATCGTTCTGGATCTT
TAACTGGATCAGTTAGTAGTTATTCAAACAAGGTTTTAGTAGTACTCGGTGCACAATGGG
GAGATGAAGGGAAGGGAAAAGTCGTGGATATGCTTTCAGTCAACGCTGACGTTGTTTGTA
GATGTCAA
>g1978.t2 Gene=g1978 Length=155
MLSIVYPIAASSTNEASMFNCFKSCTIISPSFSFLKELMLIVTYTRKCLFFEAASFNASY
TTLDRPIVKILHPSVIKSTEFLAITSRLASSFLKKLCPLLVIIFFTSSMSYISSIFGLEI
VMKHMKSSHEELIDVIGFPLSFITLIADFIVLINS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1978.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 95 | - |
| 7 | g1978.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 116 | - |
| 5 | g1978.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 117 | 135 | - |
| 6 | g1978.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 153 | - |
| 4 | g1978.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 154 | 155 | - |
| 1 | g1978.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 122 | - |
| 2 | g1978.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 132 | 154 | - |
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.
