General information for g4033.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeotic protein antennapedia.
Parent gene
- The parent gene g4033 is located on chr_3: 29784058..29793957 (- 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_3 | g4033 | g4033.t2 | TTS | g4033.t2 | 29784018 | 29784018 |
| chr_3 | g4033 | g4033.t2 | isoform | g4033.t2 | 29784058 | 29793957 |
| chr_3 | g4033 | g4033.t2 | exon | g4033.t2.exon1 | 29784058 | 29784142 |
| chr_3 | g4033 | g4033.t2 | cds | g4033.t2.CDS1 | 29784058 | 29784142 |
| chr_3 | g4033 | g4033.t2 | exon | g4033.t2.exon2 | 29784211 | 29784231 |
| chr_3 | g4033 | g4033.t2 | cds | g4033.t2.CDS2 | 29784211 | 29784231 |
| chr_3 | g4033 | g4033.t2 | exon | g4033.t2.exon3 | 29784428 | 29784572 |
| chr_3 | g4033 | g4033.t2 | cds | g4033.t2.CDS3 | 29784428 | 29784572 |
| chr_3 | g4033 | g4033.t2 | exon | g4033.t2.exon4 | 29793074 | 29793284 |
| chr_3 | g4033 | g4033.t2 | cds | g4033.t2.CDS4 | 29793074 | 29793284 |
| chr_3 | g4033 | g4033.t2 | exon | g4033.t2.exon5 | 29793430 | 29793957 |
| chr_3 | g4033 | g4033.t2 | cds | g4033.t2.CDS5 | 29793430 | 29793957 |
| chr_3 | g4033 | g4033.t2 | TSS | g4033.t2 | NA | NA |
Sequences
>g4033.t2 Gene=g4033 Length=990
ATGACGATGAGTACAAATAATTGTGAGAGTATGGCGTCATACTTTACAAATTCCTATATG
AGCTCCGACATGCATGGTCATTATCCGACTGGCGGTGACATGGACGCTCAAATGCATCAT
TATACACAGACGCATCACAATCAAACAGGAATGCCGCCATTTCCACGGTATCCGCCCTAC
GATCGTATGGGCTATTATAATCAGGCAATGGAACCCACAGGCTATTCTCGACCAGACAGT
CCATCCAGTCAAGTCGGTGTCGGTAATGTAATGGGTCCACAACAAGCACAACAGCCACCA
CCACAACAGAATGGCACAATGCAGCCATTGCAACAACAACCACCTCCACAACAGCAGCAA
CCAATCGTTTATACGAGTTGTAAACTTCAAGCTGCTGTTGGCAATAATGGTCTCGGTATG
ATAGGAGCTGATAACGGCTCACCACCACTCGAACAAATGGGTCATCACAATCATATGAAT
AATCAACAAATGCAAATGGGTCATCATATGCATGGACAAGTGAATGAAGTCGGTCATCAA
AATCCCCACAATATGGGGATGTACACGAATTCTGGAGCACCACCAGTTCAACCGCCACAG
AATATGATGCATCAGCAACCGCCTCCCATCCACCAAGGTCAACAGCAACCACAACAACAA
CAACCGCCAAATAATCATACACAAGCGTCACTTCCATCGCCGTTGTACCCGTGGATGCGG
AGTCAGTTCGGTAAGTTAGAACGAAAGCGGGGACGTCAAACATATACAAGATATCAAACA
TTGGAGCTAGAGAAAGAATTTCATTTTAATCGTTACTTAACAAGGCGAAGACGAATTGAA
ATTGCACATGCACTTTGTCTCACCGAACGCCAAATTAAAATATGGTTCCAAAATAGACGA
ATGAAGTGGAAAAAGGAGAACAAGACCAAAGGTGAACCAGGTTCAGGTGACGGTGCAGAC
GAAATTACGCCACCACAAAGTCCAGTATAA
>g4033.t2 Gene=g4033 Length=329
MTMSTNNCESMASYFTNSYMSSDMHGHYPTGGDMDAQMHHYTQTHHNQTGMPPFPRYPPY
DRMGYYNQAMEPTGYSRPDSPSSQVGVGNVMGPQQAQQPPPQQNGTMQPLQQQPPPQQQQ
PIVYTSCKLQAAVGNNGLGMIGADNGSPPLEQMGHHNHMNNQQMQMGHHMHGQVNEVGHQ
NPHNMGMYTNSGAPPVQPPQNMMHQQPPPIHQGQQQPQQQQPPNNHTQASLPSPLYPWMR
SQFGKLERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR
MKWKKENKTKGEPGSGDGADEITPPQSPV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4033.t2 | CDD | cd00086 | homeodomain | 249 | 307 | 5.29774E-26 |
| 10 | g4033.t2 | Gene3D | G3DSA:1.10.10.60 | - | 232 | 308 | 6.7E-33 |
| 18 | g4033.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 93 | 120 | - |
| 16 | g4033.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 203 | 235 | - |
| 15 | g4033.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 206 | 235 | - |
| 17 | g4033.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 303 | 329 | - |
| 2 | g4033.t2 | PANTHER | PTHR45659 | HOMEOBOX PROTEIN HOX | 11 | 316 | 2.3E-73 |
| 3 | g4033.t2 | PANTHER | PTHR45659:SF4 | HOMEOTIC PROTEIN ANTENNAPEDIA | 11 | 316 | 2.3E-73 |
| 8 | g4033.t2 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 234 | 241 | 1.5E-5 |
| 7 | g4033.t2 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 249 | 264 | 1.5E-5 |
| 4 | g4033.t2 | PRINTS | PR00024 | Homeobox signature | 270 | 281 | 6.9E-9 |
| 6 | g4033.t2 | PRINTS | PR00024 | Homeobox signature | 285 | 295 | 6.9E-9 |
| 5 | g4033.t2 | PRINTS | PR00024 | Homeobox signature | 295 | 304 | 6.9E-9 |
| 1 | g4033.t2 | Pfam | PF00046 | Homeodomain | 249 | 305 | 2.7E-21 |
| 14 | g4033.t2 | ProSitePatterns | PS00032 | ‘Homeobox’ antennapedia-type protein signature. | 235 | 240 | - |
| 13 | g4033.t2 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 281 | 304 | - |
| 19 | g4033.t2 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 246 | 306 | 21.071 |
| 12 | g4033.t2 | SMART | SM00389 | HOX_1 | 248 | 310 | 6.6E-25 |
| 9 | g4033.t2 | SUPERFAMILY | SSF46689 | Homeodomain-like | 230 | 308 | 8.13E-26 |
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:0005634 | nucleus | CC |
| 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:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09307 (homeobox protein HoxA/B7)
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. There were no conditions that were differentially expressed