General information for g11878.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein sine oculis.
Parent gene
- The parent gene g11878 is located on chr_1: 18940960..18944044 (+ 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_1 | g11878 | g11878.t1 | TSS | g11878.t1 | 18940393 | 18940393 |
| chr_1 | g11878 | g11878.t1 | isoform | g11878.t1 | 18940960 | 18944044 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon1 | 18940960 | 18941246 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS1 | 18940960 | 18941246 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon2 | 18941305 | 18941393 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS2 | 18941305 | 18941393 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon3 | 18941521 | 18941753 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS3 | 18941521 | 18941753 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon4 | 18941820 | 18941878 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS4 | 18941820 | 18941878 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon5 | 18943739 | 18943896 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS5 | 18943739 | 18943896 |
| chr_1 | g11878 | g11878.t1 | exon | g11878.t1.exon6 | 18943953 | 18944044 |
| chr_1 | g11878 | g11878.t1 | cds | g11878.t1.CDS6 | 18943953 | 18944044 |
| chr_1 | g11878 | g11878.t1 | TTS | g11878.t1 | 18944220 | 18944220 |
Sequences
>g11878.t1 Gene=g11878 Length=918
ATGGAAAATAATTGTAACGAAATTAATTTAACTGCAAACAATATCAATCAATTTATGCTT
GGACATCATAATAATTTAGACATTTCCACTATGAAGGGTGAAGAAAGTGATGAAGCTATT
CCATCATTTGGATTTACACAAGAGCAAGTTGCATGTGTATGTGAAGTTTTACAGCAAGCT
GGAAATATTGAAAGATTAGGTCGATTCCTTTGGTCATTACCAAATTGTGAAAAAATTCAA
CTCAATGAATCAGTGTTGAAAGCAAAAGCCGTTGTGGCTTTTCACAGGGGACATTTCAAG
GAGCTTTATCGGATATTAGAAAGTACTAATTTCTCACCATGTAATCATCCCAAATTACAA
TCGCTTTGGCTTAAAGCACATTACGTGGAAGCTGAAAAGTTAAGAGGACGTGCATTAGGC
GCAGTCGGCAAGTATCGAGTAAGAAGGAAATTTCCACTCCCTAGAACAATTTGGGATGGT
GAGGAAACAAGCTACTGTTTTAAGGAAAAATCACGATCAGTTTTAAGAGATTGGTATACA
CATAATCCATATCCGTCGCCTAGAGAAAAAAGAGAATTAGCAGAAGCAACTGGTCTCACA
ACAACACAGGTTTCAAATTGGTTCAAGAACAGACGACAGAGAGATCGAGCGGCTGAACAT
AATAAGGAGTCTAGTGATAAGCATTTGGATTCATCGAGTGATTCGGAATTAGAAATGCCA
GGAATGATGAGTAGTTTAGGTAATCCGAGCTCTAATAAAATGTCACAACACTCTTCAAAT
CCAAATTTACCGCACAATTTGCTGTTGCAGCAACAAGGTCAATTAGGACAAATTTCGCAA
GGATATACAGGAAGTCATTTGCACAATGCACCGCCACTTCATCCATATGACGCAATGGAT
GCGTATCAAACTTTATGA
>g11878.t1 Gene=g11878 Length=305
MENNCNEINLTANNINQFMLGHHNNLDISTMKGEESDEAIPSFGFTQEQVACVCEVLQQA
GNIERLGRFLWSLPNCEKIQLNESVLKAKAVVAFHRGHFKELYRILESTNFSPCNHPKLQ
SLWLKAHYVEAEKLRGRALGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLRDWYT
HNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEHNKESSDKHLDSSSDSELEMP
GMMSSLGNPSSNKMSQHSSNPNLPHNLLLQQQGQLGQISQGYTGSHLHNAPPLHPYDAMD
AYQTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11878.t1 | CDD | cd00086 | homeodomain | 165 | 216 | 7.08385E-17 |
| 6 | g11878.t1 | Gene3D | G3DSA:1.10.10.60 | - | 160 | 232 | 2.5E-20 |
| 10 | g11878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 204 | 238 | - |
| 11 | g11878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 209 | 234 | - |
| 3 | g11878.t1 | PANTHER | PTHR10390:SF13 | HOMEOBOX PROTEIN SIX1 | 39 | 298 | 2.4E-125 |
| 4 | g11878.t1 | PANTHER | PTHR10390 | HOMEOBOX PROTEIN SIX | 39 | 298 | 2.4E-125 |
| 1 | g11878.t1 | Pfam | PF16878 | Transcriptional regulator, SIX1, N-terminal SD domain | 45 | 155 | 2.9E-47 |
| 2 | g11878.t1 | Pfam | PF00046 | Homeodomain | 166 | 216 | 5.7E-14 |
| 8 | g11878.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 193 | 216 | - |
| 12 | g11878.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 158 | 218 | 15.256 |
| 9 | g11878.t1 | SMART | SM00389 | HOX_1 | 161 | 222 | 8.5E-17 |
| 5 | g11878.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 158 | 221 | 2.01E-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:0045892 | negative regulation of transcription, DNA-templated | BP |
| 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 |
| GO:0000976 | transcription cis-regulatory region binding | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K15614 (homeobox protein SIX1)
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.
