General information for g4028.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeotic protein deformed.
Parent gene
- The parent gene g4028 is located on chr_3: 29648153..29664693 (+ 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 | g4028 | g4028.t1 | isoform | g4028.t1 | 29648153 | 29664693 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon1 | 29648153 | 29648759 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS1 | 29648153 | 29648759 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon2 | 29650421 | 29650524 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS2 | 29650421 | 29650524 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon3 | 29650599 | 29650782 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS3 | 29650599 | 29650782 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon4 | 29663357 | 29663531 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS4 | 29663357 | 29663531 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon5 | 29663682 | 29663702 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS5 | 29663682 | 29663702 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon6 | 29664162 | 29664333 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS6 | 29664162 | 29664333 |
| chr_3 | g4028 | g4028.t1 | exon | g4028.t1.exon7 | 29664496 | 29664693 |
| chr_3 | g4028 | g4028.t1 | cds | g4028.t1.CDS7 | 29664496 | 29664693 |
| chr_3 | g4028 | g4028.t1 | TSS | g4028.t1 | NA | NA |
| chr_3 | g4028 | g4028.t1 | TTS | g4028.t1 | NA | NA |
Sequences
>g4028.t1 Gene=g4028 Length=1461
ATGAGCTCATTTCTAATGAGTTATCCTCATATGCAAGGCTCAATGGGAGGCTACGAGCCA
AAATTCCCACCAAATGAAACTGATTTTCATCACTTGCATCATCATGGCGGCTATGCAGGC
ATGAATGGATTAAGTGCGAATCATGTGGATTATTCATACCATAATGGCTATAACTATCAA
AATTATACACCAACATCCGCAACACACTCATTCTATCATCATCATCCGCCATATGGATCA
CCACAAATGCAACCGCACCATTCATCGACAAATGCCTCGTCGCCAAATTCATCACTAGTA
CCGTCAACAAATAATTCTTATAATAGTAATAATAGTAATAATAATAGTGGTAATAGTAAT
AATAATGATGGCATTGTTAGTCGAAATAATAATAATAATTTGGTGACGGCAACGACTGCC
ACAACTTTGCCAGTGCAATCGATAGTGAATGGTTTAAATATTAGTGAAAATTCACCAAAT
GTCGATAATAGTATTGGATATTATAGTAATTATTATTCTAATGGACATCAGAGTGCTCAG
GATATTCCTATACAATGTCCAAATAATGATCCACCCGCAAATACTGCTTTAGGTTTACAA
GAATTAGGTATGAAATTGGATAAGCGAATAGAAGAAGCAGTTCCTGCTGGTCAACAATTA
CAAGAATTAGGCATGAGATTGAGATGCCTTGATGATGGCAGTTCTGATCAAGACGACATG
CTCGATGATGACGATCGATTAATAATGGGCGATCGATCGCCAGATGAGCTTGGTTCACAA
GACAATGACCTCGATGATGAGCTTGATTCAGATGATGATATGGAAGGCACAACAACAAGC
GAGGGTGAACGCATTATTTATCCATGGATGAAAAAAATTCATGTTGCAGGAGTTGTGAGT
GGTCAATACTCAATGGGCATGGAAGTACCAAAGCGACAACGTACAGCGTACACGCGTCAT
CAGATACTCGAGCTCGAAAAAGAATTCCATTATAATCGTTATCTCACACGGCGCCGCCGA
ATTGAAATTGCTCACACATTAGTGCTTTCTGAACGTCAAATTAAAATATGGTTCCAGAAT
AGAAGAATGAAATGGAAAAAGGACAATAAATTACCAAATACAAAGAATGTCAAAAAGAAG
AATCCCGATGGTTCAGTTCAAGTAACGCCAGGAACAGGCAAAGGTGGAAAAGGCAAGCGT
GGTGGTGGAAAGAAAAATCAACAGCAACAACAATCAGCACAACAGCAGACATCACAGAGT
GAGTGCACGGTGGATAGTCTAGAGAGCATGACTGAAAATGGCTTAACATGTAGAAATGAT
GCATCATCATTCATTTCATCGAGTGATGTTACAGGCCTTGTATTAAATCAACAGACAAAT
GTGGCGAATAACAATAATAACCATCTTCATTTAAATGATGCCCTTAACATTAAAAGTGAT
TATGGTCTTACGACATTGTAG
>g4028.t1 Gene=g4028 Length=486
MSSFLMSYPHMQGSMGGYEPKFPPNETDFHHLHHHGGYAGMNGLSANHVDYSYHNGYNYQ
NYTPTSATHSFYHHHPPYGSPQMQPHHSSTNASSPNSSLVPSTNNSYNSNNSNNNSGNSN
NNDGIVSRNNNNNLVTATTATTLPVQSIVNGLNISENSPNVDNSIGYYSNYYSNGHQSAQ
DIPIQCPNNDPPANTALGLQELGMKLDKRIEEAVPAGQQLQELGMRLRCLDDGSSDQDDM
LDDDDRLIMGDRSPDELGSQDNDLDDELDSDDDMEGTTTSEGERIIYPWMKKIHVAGVVS
GQYSMGMEVPKRQRTAYTRHQILELEKEFHYNRYLTRRRRIEIAHTLVLSERQIKIWFQN
RRMKWKKDNKLPNTKNVKKKNPDGSVQVTPGTGKGGKGKRGGGKKNQQQQQSAQQQTSQS
ECTVDSLESMTENGLTCRNDASSFISSSDVTGLVLNQQTNVANNNNNHLHLNDALNIKSD
YGLTTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4028.t1 | CDD | cd00086 | homeodomain | 311 | 369 | 1.09449E-25 |
| 10 | g4028.t1 | Gene3D | G3DSA:1.10.10.60 | - | 281 | 370 | 1.3E-31 |
| 19 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 104 | - |
| 18 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 104 | - |
| 17 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 251 | 281 | - |
| 16 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 260 | 276 | - |
| 15 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 368 | 425 | - |
| 20 | g4028.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 403 | 425 | - |
| 2 | g4028.t1 | PANTHER | PTHR45771 | HOMEOTIC PROTEIN DEFORMED | 105 | 469 | 1.8E-67 |
| 3 | g4028.t1 | PANTHER | PTHR45771:SF6 | HOMEOTIC PROTEIN DEFORMED | 105 | 469 | 1.8E-67 |
| 8 | g4028.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 285 | 292 | 4.0E-5 |
| 7 | g4028.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 311 | 326 | 4.0E-5 |
| 6 | g4028.t1 | PRINTS | PR00024 | Homeobox signature | 332 | 343 | 4.8E-8 |
| 4 | g4028.t1 | PRINTS | PR00024 | Homeobox signature | 347 | 357 | 4.8E-8 |
| 5 | g4028.t1 | PRINTS | PR00024 | Homeobox signature | 357 | 366 | 4.8E-8 |
| 1 | g4028.t1 | Pfam | PF00046 | Homeodomain | 311 | 367 | 2.4E-21 |
| 14 | g4028.t1 | ProSitePatterns | PS00032 | ‘Homeobox’ antennapedia-type protein signature. | 286 | 291 | - |
| 13 | g4028.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 343 | 366 | - |
| 21 | g4028.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 308 | 368 | 21.637 |
| 12 | g4028.t1 | SMART | SM00389 | HOX_1 | 310 | 372 | 2.3E-26 |
| 9 | g4028.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 298 | 369 | 5.13E-25 |
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 K09304 (homeobox protein HoxA/B/C/D4)
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