General information for g5483.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5483 is located on chr_2: 9835346..9836011 (+ 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 | g5483 | g5483.t6 | isoform | g5483.t6 | 9832448 | 9834353 |
| chr_2 | g5483 | g5483.t6 | exon | g5483.t6.exon1 | 9832448 | 9832694 |
| chr_2 | g5483 | g5483.t6 | exon | g5483.t6.exon2 | 9832761 | 9833493 |
| chr_2 | g5483 | g5483.t6 | cds | g5483.t6.CDS1 | 9832768 | 9833493 |
| chr_2 | g5483 | g5483.t6 | exon | g5483.t6.exon3 | 9833613 | 9834353 |
| chr_2 | g5483 | g5483.t6 | cds | g5483.t6.CDS2 | 9833613 | 9833678 |
| chr_2 | g5483 | g5483.t6 | TSS | g5483.t6 | NA | NA |
| chr_2 | g5483 | g5483.t6 | TTS | g5483.t6 | NA | NA |
Sequences
>g5483.t6 Gene=g5483 Length=1721
TATGAAAGAATAATTTTTTTTATACTTTTGATTGCGTTCAGAAATTTTTGCAGTATTTTG
AACGCACTCTTTATCGAAGCGTTTTATGAAAATATTGAGTGTTCGTTCTCTTTTAATTTT
TCTGAATAAAACTAATAAATAGACAAAAATACGGACTACAATAAGTATATAACTGATTAT
AAGGGTCCAAATATACAAAATATACTTTTGTTTTACTGTAAAATACCGAAAAACTACAAA
AATAAAGTCACAAAATGCCGCGAAAAGCAAGAGGATCGGGAAGCTCACCCGAAAAGCAGA
CAACTACAAGAAGAAATACTCGTCGAGGACAAAAAGTTTCTGAGCCAGCTGAAAACGAAA
TTACCGATGAAATCCCGGCTCATTTGCTGAGAGGATCTGATGAATCTTCTGAACAATCTG
ATAATGATTCTGATTATGGCAGCCCAAAAAAGGGTAGAGGAAGAGCAGCTGCAACTAGGG
GTCGTGGCAGAAAAGCAAAAGAGGCAGAAGAAAAGACTGCACCTACTCCGAGTCGACCAA
GACGCGGAAGACGAGCAAGAGGAGAAAGTCCAGCAACAATAGATGAACAAGAACAAGAGC
AAAACTCACAGGAAGAATATGTTGAATCTGTTAACAGTCAAACAACAATTGAAGAACATG
AAACTTCTACTATGGAATCAACATCTGATCAACGAGTTGTTTCTGATGAAAAACAAGAAG
AACAAGAAATAGAAAATGTTCAAGAGTCTTTTCCTGAAAAAAGTGTTGAACCAGAGAAAG
AATCGTCACCAAAGAATGAGGAACCACAAGAAATCATTGAAGTGAAAGAGCAAGTAATTA
CTGCTGAAAAGGTAAGTGAAGTAACAATTGAACAGGATCAATCGAATAATGATCAAGCAA
CTGTTAACGAAGAAGTTGTTGCTGATGATGATGAAAGTAAACAAAATGAAGAGAGTCAAA
ATGATGACAATGTAGAACAGTTCACCTCAACAACATACGAAAAATCAATTACAACGTTCA
AGATCAAGTTCAGGAGAAATCCATGAAGATAGCAGAGATGAATCTATGAAAGAAAGTTCG
CCAAAAAAGCCACAAGAATCATCTCCAAAGAGAAATCAATCTCCAATAAAGCAGCCGTCA
CCAAAAGAGACAGAGCCTAAACCTGTGACTCAAAGAAAACGAAAATGGGGTGCACGTAAA
GATGATGAAAAAGTTATTGCTATAACTACAGATTCATTGGCAAATATTATCGCTGAAGAA
GTTAAACCAGTTCCTTTAAGTGATGTAAAATTAGCAATGAGTCCATCACCTGAACCAGAA
GAAAAAAGACCAAGAGTTAGACTTTCATCGGAAGATCGTGATGCAAAAAAGAAACTTTTA
AAGGAACGTTTGAGAAAACAAGAAGAAGAAGAGGAACGTCGAAATGAGCAAATTGCTAAA
GCTAGTGAACGCAGTCAAGTATCTCCGACAATTGTTGTCACAAATGGAGGTGCTGGAAAA
GATCGTAAAGTGTCACTTGTTAGCAATGAAGAAGCGATTGCAAAAACTTCATCCTCGCCA
ATATCGAAAAATCAATGCTCAAAAGTTATATGTATCACAAATTTGGTACGTCCTCTAACA
TTTTTAGCTGTCAAATCTTTGGTCTCACGAACTGGTGAACTTGATGATTTTTGGATAGAT
TCTATCAAATCAAAATGCTTTGTAAAGTACAAAACAGAAGA
>g5483.t6 Gene=g5483 Length=263
MPRKARGSGSSPEKQTTTRRNTRRGQKVSEPAENEITDEIPAHLLRGSDESSEQSDNDSD
YGSPKKGRGRAAATRGRGRKAKEAEEKTAPTPSRPRRGRRARGESPATIDEQEQEQNSQE
EYVESVNSQTTIEEHETSTMESTSDQRVVSDEKQEEQEIENVQESFPEKSVEPEKESSPK
NEEPQEIIEVKEQVITAEKVSEVTIEQDQSNNDQATVNEEVVADDDESKQNEESQNDDNV
EQFTSTTYEKSITTFKIKFRRNP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5483.t6 | Coils | Coil | Coil | 109 | 129 | - |
| 6 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 248 | - |
| 5 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 17 | 65 | - |
| 3 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 109 | - |
| 4 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 137 | - |
| 2 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 196 | - |
| 1 | g5483.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 218 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5483/g5483.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5483.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.
