General information for g16068.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeobox protein SIX4.
Parent gene
- The parent gene g16068 is located on chr_4: 7965713..7967433 (- 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 | g16068 | g16068.t1 | TTS | g16068.t1 | 7965073 | 7965073 |
| chr_4 | g16068 | g16068.t1 | isoform | g16068.t1 | 7965713 | 7967433 |
| chr_4 | g16068 | g16068.t1 | exon | g16068.t1.exon1 | 7965713 | 7965854 |
| chr_4 | g16068 | g16068.t1 | cds | g16068.t1.CDS1 | 7965713 | 7965854 |
| chr_4 | g16068 | g16068.t1 | exon | g16068.t1.exon2 | 7966460 | 7967433 |
| chr_4 | g16068 | g16068.t1 | cds | g16068.t1.CDS2 | 7966460 | 7967433 |
| chr_4 | g16068 | g16068.t1 | TSS | g16068.t1 | NA | NA |
Sequences
>g16068.t1 Gene=g16068 Length=1116
ATGGATTCATCATTACAAGATCAAAATCAACCACAACCATTACATATTCCTTTAAATTCA
ACATCAGCTGCAATTGCTTCAATGAATTTACCACCACTTCAACATCTTGACGTTCTAGAA
AATCAAGAAGCTTCAAAAGCAATGATGAGTTACATGTCAATGCAGCAGCAAGTCAGTGCA
CTTCAACCATTACAAAGAAATAATATTTATGATCAAACAGTGGAAAATTATAATGACAAT
TATGCACTAAAAATGAATAATAATAAAATTCAAACTGGAATAAAACGAAAAGCAGATTTT
GATGATCCTTATGTTGCATTTAAACGCAAACCTGACTTTGATGATCAAAATCTTGCTTAT
AAACATGTTGAAAATAATGAAAATCTTTTGCCATCATCAAATATGGAAATTAATCTTGAG
CTCAATAAAAAATTCTTTTCATTTACACCAGAACAAGTTCAATGCATGTGTGAAGCATTG
CAGCAAAAAAATGATCTCGATAAATTGACAACTTTTCTCTTCAGTCTTCCACAAGATGAA
TTTCTCGGCAATAATGAGTGTATTTTAAGAGCAAGAGCTAATGTTGCTTATCATCGTGGT
TCCTTTCATGAACTCTATGGCTTACTTGAAAATCATTGCTTTTCGGTCAAATACCATCCA
CATTTGCAAGAATTATGGTTTAAAGGTCATTACAAAGAAGCTGAAAAAGTTCGTGGACGT
CCACTTGGTGCTGTTGATAAATATCGATTAAGAAAAAAATATCCATTGCCAAAAACAATT
TGGGATGGTGAAGAGACAGTTTATTGTTTTAAAGAAACTTCAAGAAATGCATTAAAAACT
TGCTATGAAAGAAATCGTTATCCGACGCCTGATGAGAAAAAAGTTTTAGCTAGAAAGACT
GGATTGACATTGACACAAGTTAGCAATTGGTTTAAAAATAGAAGACAAAGGGATCGAACT
CCACAGGCAAGAAGTGAATACATGCATTTGTCAATGAATGATGAAAGTTTCTCGAGCAGA
ATTTATGCACCATTTGCAACAAGTACAACAAATTCTAGTGGACAGTTTCATCCAAATCTT
TATGCAACTGATCAAAAATTTGGACAAACTGTTTAG
>g16068.t1 Gene=g16068 Length=371
MDSSLQDQNQPQPLHIPLNSTSAAIASMNLPPLQHLDVLENQEASKAMMSYMSMQQQVSA
LQPLQRNNIYDQTVENYNDNYALKMNNNKIQTGIKRKADFDDPYVAFKRKPDFDDQNLAY
KHVENNENLLPSSNMEINLELNKKFFSFTPEQVQCMCEALQQKNDLDKLTTFLFSLPQDE
FLGNNECILRARANVAYHRGSFHELYGLLENHCFSVKYHPHLQELWFKGHYKEAEKVRGR
PLGAVDKYRLRKKYPLPKTIWDGEETVYCFKETSRNALKTCYERNRYPTPDEKKVLARKT
GLTLTQVSNWFKNRRQRDRTPQARSEYMHLSMNDESFSSRIYAPFATSTTNSSGQFHPNL
YATDQKFGQTV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g16068.t1 | CDD | cd00086 | homeodomain | 268 | 322 | 1.68361E-14 |
| 6 | g16068.t1 | Gene3D | G3DSA:1.10.10.60 | - | 268 | 329 | 1.5E-17 |
| 3 | g16068.t1 | PANTHER | PTHR10390 | HOMEOBOX PROTEIN SIX | 145 | 326 | 5.0E-97 |
| 4 | g16068.t1 | PANTHER | PTHR10390:SF64 | SIX HOMEOBOX 4A-RELATED | 145 | 326 | 5.0E-97 |
| 1 | g16068.t1 | Pfam | PF16878 | Transcriptional regulator, SIX1, N-terminal SD domain | 148 | 258 | 1.1E-43 |
| 2 | g16068.t1 | Pfam | PF00046 | Homeodomain | 269 | 319 | 6.8E-14 |
| 8 | g16068.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 296 | 319 | - |
| 10 | g16068.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 270 | 321 | 14.479 |
| 9 | g16068.t1 | SMART | SM00389 | HOX_1 | 263 | 325 | 2.7E-16 |
| 5 | g16068.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 261 | 327 | 4.18E-18 |
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:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K15615 (homeobox protein SIX4)
Pathway
- This transcript belongs to the following pathways
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. There were no conditions that were differentially expressed