General information for g1972.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1972 is located on chr_3: 14156107..14161713 (+ 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 | g1972 | g1972.t2 | isoform | g1972.t2 | 14149456 | 14153839 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon1 | 14149456 | 14149562 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon2 | 14149629 | 14149857 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon3 | 14149920 | 14150276 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon4 | 14150348 | 14152075 |
| chr_3 | g1972 | g1972.t2 | cds | g1972.t2.CDS1 | 14150831 | 14151223 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon5 | 14152130 | 14152269 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon6 | 14152348 | 14152706 |
| chr_3 | g1972 | g1972.t2 | exon | g1972.t2.exon7 | 14153618 | 14153839 |
| chr_3 | g1972 | g1972.t2 | TSS | g1972.t2 | NA | NA |
| chr_3 | g1972 | g1972.t2 | TTS | g1972.t2 | NA | NA |
Sequences
>g1972.t2 Gene=g1972 Length=3142
TCACTGTATGTAGAGTGTGTTTAAAACCAACACGTGATGATTATTCTTTGCCAATGTGAC
AATATATCCTTCGCTTGTAATTTTCAGTCCACAGCATCGTGAAACCTAACATATGGACAT
TCGTATTCGCATTGCAAAACACCGTAACGATTATAGCATGCAACGTGGAATCGATTGCCA
TGAGAGTCGCCGATTAAAATATCGCCAGCATCAGAAATATCAATTCCATTAGGAAAGCAT
GTTACTTTTTCACTTCCAATTCGGGTCTTAAATTGACCTGTCTCGCTAAAAACAGCAACA
CAATGTCCCTTGAAGTCGCACACATAAAAATCATTTCCGTTGATTGCTATATCTGATGGT
TCACGCATATGATCACTGCAATCAAACCAATGAACCAAATCACCATCCTCAGAGATAATG
AAAACAGTTGGTGAAACGCTATCAACAGCAACAATATGACCTTGTTGAGTGACAGCTAAA
CCAGCAACAATGTCAATGTAGCGAATAGCAATTTTCTTTATATAATGACCATTCTTTGTA
AAAATTTGCATACGAGATCTCTCATTACCACGATCACATACTACAAATTTGCTGTTGGGC
CTCATAACTGCAACTTTTCGTGGAAACCATAGTTGTCCTTCCTCCTTTCCTGGCACACCA
AAATGAAATTTGTATGTTCCACTTTTATCGAAAACTTCAATTCGATGATTATTAGTGTCT
GCAACAATAATTTCTTCATCTAAACCCAAGCAAAAACCATGGGGCGAATTAAATTGTCCA
CGCGATTGACCGAGTGCGCCAAATTTCACTCGAATTTGCATTGATAAAGCTTTTGGACGA
CCGATACCATTAGAGCTTGCAGACGTATTTTGATTGCTGTCGTGAGTGCGGAATTGAGAA
AAACAATTCAATTTCATGTCATCATTGATTGCAGCGAGAGTTGATGGTGTTTGAAGAATT
GGCGAAGGTGAGGTCATAAATGAATCCATCATACCAAGATTATTCAAGTTATTTATAGCA
TTTCCATTGTTCATATCACCAATCTTGGCTAGTGCTTGCAAATTATTGAGCATTTGTTGA
TCACCATTGAGCATTTCTTCAAGAAGAAAATTTGTGCCTACAGTAGAACCAGCAGGAATA
ATTGTTTCATTTAAATCAGATGTTGTGCTTTCAACCATGCTTGCAGCCAAACGATGCAAA
TTGTACTCAACCATACTGCTAACAGGTGGTGTAACAACATTGAGTTGTGCAGTAGCAGCT
GGAACGATTGGTGTAGGTGACTCAGGAGTTATTAAACTTGCAGGCATGAGTGATGAAAAG
TTCTTTCCAAATCCACTTATGCTGTTGCTAATATCGCCATCGAATGAAGATTGTAATGAA
GTTGGCAAGGAAATAGGACTACTAGCTGTAACTGAAACACTACCAGTAGTGATTGAGCTT
CCGTTTCCACTTGAACTACCATTTGTCATGATAGTTGAACTCTTAATAGTGCTTTCGTGC
AACGAAGGCATACTTGGAAGCGTTGGTGGAGGTGTAGCCTCTTTAGGAATGATAGTTGAC
TCTGTTTGAAACTTGCCAAATAATTTTGGTACCATTTCTTGGAATTTATTTGTATTTGAA
ATAAATTCCAAAGAATAGTTCGCATCAATCTTTGGAATTTTACCGATTAATTTCATCAAT
TGCAAACTAATCATTTTCTTCATGCTTAAAATCTCATGACCATTGCCATTATCCAAAAGT
TTTCGAGTGAACATCGCACAATATTCCATTTGCTCAACAGTATTTTCAATTTGATGAAGT
TGTTCCATGATTTTAATCTCGCGTTCAGCATGCAAACTTCCCAAATCCAACAACATTTGC
TCCTTTCGCTTTTCGATTGCACTAATTATTACGTCGTATGCTTTATTGATTTCATTTCGA
GCAGTATCATGTTTTTGTTGCAACTCTTGCAAAGATGCGACAAGTTTTGAGTTCTGAACA
TCGCAATAATCAATTTTGCCTCGAGTATTCTTTAATAAATTTTCAACGTCCATGCGCATA
CTCTTTTCAGCCTCACTTATGACTTCATAGCGATGTTCGGTCGCTTTATGATCAGAAATT
AGACACTCATTGCACACTGGAGTCTCGCAGCTGTAGCAAAAATACTTAAGATTTTCTGTT
GCATGAACGCTACAGTATAGAGGTTTATGAATAGTTCCACTCGCTTCCAATGTAACAACT
TGATGTTCTTCAAAACATCGCATAGTACGATGAGCTTTATCGCAATCAGTGCAAAGAAAA
TTGGCACAACCATTGCAGCGCGAGATTGCTTCCTCCTTGCTCTTGCATGATGTGCACAAT
AATGTGCTGATATCAGTTGTTGCAAGATCAAGGATGTTAGTCAAAATAAAATGGAAAGGT
AGAGATGAAGGACCTCTTGGATAACGTACTTTGGTTATTTGATCACAAGTTGGACACTCA
ATTACGGCTTCTTCCGATGAGTCTTCCAATGATAATTTTGAGATGCATGGATCGCAAAAG
AAATGTAAGCATGATAAAACACGAGGTAGAATCAATTTTTTCTGGCAATTCTTGCAATTT
TCATCTTTACCATCATTCACTCCTTCAAGTGGTTCAACAGCAACTTCTTCACCATTGCCG
TTTGTTGTAAAAGTCTCACCCGAAAAAATATTCTCAGATACACTAACAGTTGATGTTGTC
GTCGTTATTGATGAATCAGTAGAAGAAGTAGGTAAGGGAGATGATGGTGATGATGAAATC
GGCGATGGCGATGGTGCTGTATCCACAAGCTCCATTACTCTCCAATAAATAAATTAGTAG
TTTGTTATTGATTTTGGGAAATAATATTTAGGCCTCTTAGTTGCTTTGTGTTGTTGTGTT
TTCTCGTAAAATGATCGTTTCTTTCATAAACTTAAACAAACAAAAATTTATTTTTTATTT
TAGAAAATTTTCTCGATTTCTGCTTTTAGAGACCACTCAACTTACCCCGCAAATTCACTT
GCCCCTTGAATTTTTTTTTTAAATTTAAAATTGGCGCTTTATTTTCCGTTAGGAAATGCA
CAAAAGATATTTTCATTTGAAGTGAAGATAAACAAAGTACTTTTTTCCGAAAAAAAAGAA
TTAAATAATCGTGTATGAAAGA
>g1972.t2 Gene=g1972 Length=130
MLAAKRCKLYSTILLTGGVTTLSCAVAAGTIGVGDSGVIKLAGMSDEKFFPNPLMLLLIS
PSNEDCNEVGKEIGLLAVTETLPVVIELPFPLELPFVMIVELLIVLSCNEGILGSVGGGV
ASLGMIVDSV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1972.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 27 | - |
| 7 | g1972.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 10 | - |
| 8 | g1972.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 11 | 22 | - |
| 9 | g1972.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 23 | 27 | - |
| 5 | g1972.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 130 | - |
| 4 | g1972.t2 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 24 | 6.0 |
| 1 | g1972.t2 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 27 | - |
| 3 | g1972.t2 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
| 2 | g1972.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
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.
