General information for g5926.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5926 is located on chr_2: 12880705..12881875 (- 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_2 | g5926 | g5926.t6 | isoform | g5926.t6 | 12878379 | 12881579 |
| chr_2 | g5926 | g5926.t6 | exon | g5926.t6.exon1 | 12878379 | 12879221 |
| chr_2 | g5926 | g5926.t6 | TTS | g5926.t6 | 12878406 | 12878406 |
| chr_2 | g5926 | g5926.t6 | cds | g5926.t6.CDS1 | 12878909 | 12879221 |
| chr_2 | g5926 | g5926.t6 | exon | g5926.t6.exon2 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t6 | cds | g5926.t6.CDS2 | 12879294 | 12879653 |
| chr_2 | g5926 | g5926.t6 | exon | g5926.t6.exon3 | 12879723 | 12880168 |
| chr_2 | g5926 | g5926.t6 | cds | g5926.t6.CDS3 | 12879723 | 12879949 |
| chr_2 | g5926 | g5926.t6 | exon | g5926.t6.exon4 | 12881471 | 12881579 |
| chr_2 | g5926 | g5926.t6 | TSS | g5926.t6 | 12881780 | 12881780 |
Sequences
>g5926.t6 Gene=g5926 Length=1758
ATGGACTCAGAAATGATTTTAAATCTCGTAATAAAAGTCCAGCAATTTGAGGACAAACGA
ATTGAGGCGAAAGCATCATGGAATATAAGAGAATTAAAAGGAAAACTTAAGCACTGAAGA
ACAGAAACTTATATATTCTGGAAAGCTCTTGAACGATACTGTTATATTAAAGGACGTTTT
ACGAGAATACGAAGGACAAGAGGCTCATACAGTTCATTTAGTTTTCACACCCAAACAAAA
TTCGCGTATTCAAAATAAATTTCAGGAAAGCAAACAAAATTCATCTGTCAACTCCATTAA
TAACCAGACATCATCATCGTCATCAGATATGAGTACAAGCGAATTAAGACAGAGACATAC
AGCTACTGCCACTGTTGCTCCTAACAATACAACTGAACAACAACAGATGACTTCTAGTAG
CAACATTCCTAATAATTATTTTAATGCTTTCTATGGTAATACAATGGACGCTAATAATAT
TTTGGCTCAACAATATGCAATGCAAACATGGATGCAACAAGCTTATGCTCAGTATATGAG
TCAATATATGAATATTATGTCACAATCAGAGCAACAAGCTAATGCTCAAACAACAAATTT
TGCTTTTATGCAGCCTCCAATGCCTTCTATACCAACTCCAACTACAGTGACTCCATCAAC
ACAATCGCCAAATGCTGAAACTCAAGCAGCATCTGCAACTCCTGTAGCGGAACAACAACA
AGCACAACAGAATCAACCTGCAGCCGAGCCACAACGTCGATTTCCAAACATCATTCAAGA
TGAGCAGGAAAATCGTGATTGGCTTGATATTCTTTATTCAATGTCTCGTCTTATGATACT
TTTGTGTCTTGTCTATTTTTATTCGTCGCCTCTTAGATGTCTCATTGTAATTCTCATAGG
TGTATCAATTTATTTATATCACATTTACAAACAAAATCAAAATCGTCTTAATAACAATAA
TACAAATCGTGTTAATTTAAATGTAAATAACAATCAACCAGCTGCTGCTGCACCACAACA
ACCAGCACCAGAAAATAATGAAAATCCTGAACAAAATAATGAGAGTCAATCAAATCAGTC
ATCACTTTCTGAAAGTATTAGTGAAAGTGAGCCTTTAGTGAATGAAATTTCTCAAAACGA
AGAACCACCAGTTTCAATGTTGACAGTGTTAAGAACTTTTGTTATATCATTTGTAGCTTC
AATTATTCCAGAGCATCCCGCAATGTGAGAGAATTTCATATTGTTTATGGGCATTTATTT
GGTAGTTTACATAATTATATCTATTTTTAAAATAGTTAGAGAAGCAAATGTTCTTGACTA
ACTCCACTGAGGGATTGAAAACACCGTATATTTGTTATTGATTAAACTTTCGCACTGAGA
CTAATGAACTAATCGTTTGTTCACCTCAATTGTTCCTTTATTTAGTGTGCTGACAAAAAA
ATTAAAGTGGTATTGCAGCGGTAACTATTGTTATAAAAAATTATATTTTTATTTAGTTCA
TTAACACTAAATGAATGAAAGAAAAATATGAAAATATTCTTTCAATATTAATTATTTATT
TATGAGAATGTACCTTTAATCCCTTGGCTTCAAACACACATCCGTGTTTAAAAGTTTTAA
TTTAAGTTTTAAAAAACTGTGTTAGATAAAATACAAAATAAATCTTGTAACAACTTCCTT
ATCATAGATAAAAGAGGAATAAAAAAAAAGTTTTATTGATGCATAATAAAAATTGTGAAT
TTATTTAAATTGAAAAAT
>g5926.t6 Gene=g5926 Length=299
MSTSELRQRHTATATVAPNNTTEQQQMTSSSNIPNNYFNAFYGNTMDANNILAQQYAMQT
WMQQAYAQYMSQYMNIMSQSEQQANAQTTNFAFMQPPMPSIPTPTTVTPSTQSPNAETQA
ASATPVAEQQQAQQNQPAAEPQRRFPNIIQDEQENRDWLDILYSMSRLMILLCLVYFYSS
PLRCLIVILIGVSIYLYHIYKQNQNRLNNNNTNRVNLNVNNNQPAAAAPQQPAPENNENP
EQNNESQSNQSSLSESISESEPLVNEISQNEEPPVSMLTVLRTFVISFVASIIPEHPAM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5926.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 30 | - |
| 7 | g5926.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 104 | 149 | - |
| 6 | g5926.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 105 | 141 | - |
| 4 | g5926.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 269 | - |
| 1 | g5926.t6 | PANTHER | PTHR12943:SF27 | HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A | 3 | 298 | 1.4E-31 |
| 2 | g5926.t6 | PANTHER | PTHR12943 | HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER | 3 | 298 | 1.4E-31 |
| 9 | g5926.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 157 | - |
| 11 | g5926.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 178 | - |
| 10 | g5926.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 179 | 183 | - |
| 12 | g5926.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 200 | - |
| 8 | g5926.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 201 | 299 | - |
| 3 | g5926.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 175 | 197 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5926/g5926.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t6.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.
