General information for g16603.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g16603 is located on chr_4: 10172107..10174064 (+ 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_4 | g16603 | g16603.t2 | isoform | g16603.t2 | 10171174 | 10172107 |
| chr_4 | g16603 | g16603.t2 | exon | g16603.t2.exon1 | 10171174 | 10172107 |
| chr_4 | g16603 | g16603.t2 | cds | g16603.t2.CDS1 | 10171358 | 10172107 |
| chr_4 | g16603 | g16603.t2 | TSS | g16603.t2 | NA | NA |
| chr_4 | g16603 | g16603.t2 | TTS | g16603.t2 | NA | NA |
Sequences
>g16603.t2 Gene=g16603 Length=934
AGAGTTTCATAATTTCATCTAGATATGACAAGTGAGTTTCAATTTTATTTGAATTTTTAC
TTTAATAAATCATTTTAGTACACGAATTTTAATTAAATTTATCCCTAATAATGTTTGGTA
TCATCCACAGTTATTGAAATTTAAAAACATTTCCAAATAAAACTAAAAATTATAAAATTT
TAAAATGAACAATAAAAATAAACAAAGTTGGAAACCTGAAGTAGATAAAATCTATACAGG
TGAAGTTATTGATGTCCTAAATCATGGAGCAATGGTTCGATTAAAAGGCTTTGGTGGTGG
ACGAGGACGTCGAGAATTCAAAGGGCTTTTGCACAACAAAGACTCACCGATTGTTGAAAA
ATTGATCGATGGACATAAAGTTAAAGTTCGTGTCATTGCATTTATGCCTGATGGTTTTAT
TTCAATTACAACCAAAGACATTGAGCAGCCAGAAAATGAAACTGTAAATGTTTTTGATGA
AGCTTATGAGAAACAAAGACAAAAAATTCGTGTAATGAGTCCAGAGAGAAGAGATGTCAA
TCAATTTACAACTCCAAAGTCTGTAAGCATCGAAGTGATCACAACTGAGCCAGATTTTCT
AAAAAATGTCAATTTAAGAATTCCTTCGAGAATTCCAACAAAAATTTCGATTTACAAAAA
TGAAAACAGTTTTATGGCAGAAGTTGCAAAAGAAAAGAGCAAAAATAATCAAGATTTAAA
GTTTCAGCGTGGAAGTTTCGATTCTAAATGGATTGATCCAGTTCGAATGAATTCACAAGC
AACTGAAAGTTTTGAAAATTCAACTCAGCCAGAACCGATGAAGAATCGAAATTTAATGTC
AATTACAGAACAACGTGAATCACTTCCAATTTTTAAATTTCGTAATGAAATTATTCGATC
AGTTGTTGAAAATCAATTTTTAATCATTCAAGGC
>g16603.t2 Gene=g16603 Length=250
MNNKNKQSWKPEVDKIYTGEVIDVLNHGAMVRLKGFGGGRGRREFKGLLHNKDSPIVEKL
IDGHKVKVRVIAFMPDGFISITTKDIEQPENETVNVFDEAYEKQRQKIRVMSPERRDVNQ
FTTPKSVSIEVITTEPDFLKNVNLRIPSRIPTKISIYKNENSFMAEVAKEKSKNNQDLKF
QRGSFDSKWIDPVRMNSQATESFENSTQPEPMKNRNLMSITEQRESLPIFKFRNEIIRSV
VENQFLIIQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g16603.t2 | Gene3D | G3DSA:2.40.50.140 | - | 12 | 92 | 0.0000140 |
| 3 | g16603.t2 | Gene3D | G3DSA:3.40.50.300 | - | 159 | 250 | 0.0000086 |
| 5 | g16603.t2 | ProSiteProfiles | PS50126 | S1 domain profile. | 14 | 84 | 9.2670000 |
| 2 | g16603.t2 | SMART | SM00316 | S1_6 | 12 | 84 | 0.0000035 |
| 1 | g16603.t2 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 9 | 87 | 0.0000217 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003676 | nucleic acid binding | MF |
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.
