General information for g9639.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Visual system homeobox 2.
Parent gene
- The parent gene g9639 is located on chr_1: 4423701..4424405 (- 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 | g9639 | g9639.t1 | TTS | g9639.t1 | 4396190 | 4396190 |
| chr_1 | g9639 | g9639.t1 | isoform | g9639.t1 | 4396545 | 4423701 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon1 | 4396545 | 4396890 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS1 | 4396545 | 4396890 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon2 | 4397000 | 4397525 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS2 | 4397000 | 4397525 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon3 | 4397732 | 4397894 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS3 | 4397732 | 4397894 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon4 | 4398033 | 4398044 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS4 | 4398033 | 4398044 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon5 | 4411345 | 4411403 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS5 | 4411345 | 4411403 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon6 | 4411477 | 4411544 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS6 | 4411477 | 4411544 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon7 | 4411618 | 4411702 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS7 | 4411618 | 4411702 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon8 | 4417299 | 4417343 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS8 | 4417299 | 4417343 |
| chr_1 | g9639 | g9639.t1 | exon | g9639.t1.exon9 | 4423278 | 4423701 |
| chr_1 | g9639 | g9639.t1 | cds | g9639.t1.CDS9 | 4423278 | 4423701 |
| chr_1 | g9639 | g9639.t1 | TSS | g9639.t1 | 4424467 | 4424467 |
Sequences
>g9639.t1 Gene=g9639 Length=1728
ATGAATCTTGATTCTTTAATTTCATCATCTGCAATTCGTTCAGAGACATTAACTGCAACT
TTAAATCGACATAATTATCCAACAGCACATCAAACAATGCCACAAAGATCGCCATTCGCA
ATTCAAGAGCTTCTTGGTCTCGGTCATAGTGATTCAGCTCGTCAATCTTCAAATGGAAGT
TCAAATAATTCAAGTGCACCAAGTGCAACTAGCAGTGCTAGTGGTCCAGTGTCAGCAGTT
ACTCCTTCAATTTATTCACAAACAAATTCAGTTGATCATCATCAGATGCAAATGGCAGCT
TCAAGAATGGCATATTTTAATGCACATGCCGCTGCTTTTAATGTTGCTGCAGCATTTTTA
CCACATAATATGACTTCAGCAGGAGCTGGCGGTCCATTAGCTGGTCTTCATCCACAAGCT
GCTGGTTTTCCGCAACTAAAGACATCGTTTGGTACAGCAAATATTCCAGCAACACCAATT
GATCCAAGCAAAGAATTCACAGTTGATGGTATTAATGGCTTCAGTAAAAAGAAGAAGAAA
AAGCGACGTCACAGTCGAACAATTTTCACAAGCTATCAACTAGATGAGTTAGAAAAGGCA
TTTAAAGAGGCTCATTATCCAGACGTTTATGCCCGCGAAATGCTATCGCTAAAAACAGAT
CTACCAGAAGATAGAATACAAGTTTGGTTCCAGAATCGTAGAGCAAAGTGGCGCAAAACT
GAAAAATGTTGGGGTCGTTCAACAATTATGGCAGAATATGGACTCTATGGAGCTATGGTT
CGTCATTCTCTTCCATTACCTGAAACAATTTTGAAGTCAGCAAAAGAGAATGATTGTGTT
GCACCTTGGCTTCTTGGTATGCACAAAAAATCAATTGAAGCTGCTGAGACACTTAAAAGT
GGAGATGAAAATAGTGATAAAGAAGATGAAGCTGAAACTGAAGTTAGTGATACAAGCTCA
TCAAATAACAACAATAATAATCGAAAAACACCAACGACACCAAATTCTGCATCAGCACCG
AAATCGAAAATTACATCGAATGGTTCTCCTTCATGTTCTAGCTCAATCTCACCCGTAACT
ATGTCACCACCAATTACAAATCATTCTTCAACAACGCCCACACAACAACGTTCATCTGAG
GATCTAACAACTAATACCAAAAAGGATTATAATTTGATGTCGAGTCCTTCTGCAACCAGA
GGACCACCTTCAAATGGTCCAGCCAATTATTTGAATCCACATGAGTCTAATACAACACTT
GCACATCATCCTCATCCTGCTCATCATTATCCATTGAATCCTATCAACCCATCGCCTGAC
ACTGATCCAGAAGTGTTTAGGTGGGTCAACTACAATCGCGATATTCCTGTTTCTTTTATA
CGAAATAATTCAATTGCATGTTTACGTGCAAAGGCTCAAGAACATCAAGCAAGATTAATG
AACAGTGGACTATTGGCACTTCAAGTTAGATCTCTAGCTGGTCTTCAACAGCATCATCAA
TTACCAAGTCCAATGAGCAGCTCACCAGATAGTGTTATGATCCACCAACATTCACCAAGT
CCTTCGCCAATAAGATCGCCTGAAAGTAACAACAATAATAATAGTAGCAGCAGGAATTTT
AATTCAAGCATGACACATTCGAGTGATGTTAGTGAAGATATAGATATCGAAGAGGTTAAG
CCTTTTCACAACAAATCAAATGCAAGTCCAAATGTAGTTACATTTTGA
>g9639.t1 Gene=g9639 Length=575
MNLDSLISSSAIRSETLTATLNRHNYPTAHQTMPQRSPFAIQELLGLGHSDSARQSSNGS
SNNSSAPSATSSASGPVSAVTPSIYSQTNSVDHHQMQMAASRMAYFNAHAAAFNVAAAFL
PHNMTSAGAGGPLAGLHPQAAGFPQLKTSFGTANIPATPIDPSKEFTVDGINGFSKKKKK
KRRHSRTIFTSYQLDELEKAFKEAHYPDVYAREMLSLKTDLPEDRIQVWFQNRRAKWRKT
EKCWGRSTIMAEYGLYGAMVRHSLPLPETILKSAKENDCVAPWLLGMHKKSIEAAETLKS
GDENSDKEDEAETEVSDTSSSNNNNNNRKTPTTPNSASAPKSKITSNGSPSCSSSISPVT
MSPPITNHSSTTPTQQRSSEDLTTNTKKDYNLMSSPSATRGPPSNGPANYLNPHESNTTL
AHHPHPAHHYPLNPINPSPDTDPEVFRWVNYNRDIPVSFIRNNSIACLRAKAQEHQARLM
NSGLLALQVRSLAGLQQHHQLPSPMSSSPDSVMIHQHSPSPSPIRSPESNNNNNSSSRNF
NSSMTHSSDVSEDIDIEEVKPFHNKSNASPNVVTF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9639.t1 | CDD | cd00086 | homeodomain | 183 | 241 | 2.34524E-22 |
| 5 | g9639.t1 | Gene3D | G3DSA:1.10.10.60 | - | 175 | 243 | 3.2E-29 |
| 10 | g9639.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 77 | - |
| 11 | g9639.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 296 | 382 | - |
| 13 | g9639.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 316 | 382 | - |
| 9 | g9639.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 497 | 575 | - |
| 12 | g9639.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 497 | 549 | - |
| 3 | g9639.t1 | PANTHER | PTHR46892 | VISUAL SYSTEM HOMEOBOX 2 | 34 | 513 | 1.2E-114 |
| 2 | g9639.t1 | Pfam | PF00046 | Homeodomain | 183 | 239 | 7.5E-22 |
| 1 | g9639.t1 | Pfam | PF03826 | OAR motif | 461 | 476 | 2.4E-6 |
| 7 | g9639.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 215 | 238 | - |
| 16 | g9639.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 180 | 240 | 19.143 |
| 15 | g9639.t1 | ProSiteProfiles | PS51496 | CVC domain profile. | 242 | 293 | 22.931 |
| 14 | g9639.t1 | ProSiteProfiles | PS50803 | OAR domain profile. | 463 | 476 | 10.509 |
| 8 | g9639.t1 | SMART | SM00389 | HOX_1 | 182 | 244 | 6.5E-25 |
| 4 | g9639.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 175 | 241 | 1.75E-23 |
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 K09336 (visual system homeobox protein 2)
Pathway
This gene does not belong to any 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.
