General information for g4025.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeotic protein proboscipedia.
Parent gene
- The parent gene g4025 is located on chr_3: 29581582..29583748 (- 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 | g4025 | g4025.t1 | isoform | g4025.t1 | 29581582 | 29583748 |
| chr_3 | g4025 | g4025.t1 | exon | g4025.t1.exon1 | 29581582 | 29582607 |
| chr_3 | g4025 | g4025.t1 | cds | g4025.t1.CDS1 | 29581582 | 29582607 |
| chr_3 | g4025 | g4025.t1 | exon | g4025.t1.exon2 | 29582910 | 29583235 |
| chr_3 | g4025 | g4025.t1 | cds | g4025.t1.CDS2 | 29582910 | 29583235 |
| chr_3 | g4025 | g4025.t1 | exon | g4025.t1.exon3 | 29583294 | 29583411 |
| chr_3 | g4025 | g4025.t1 | cds | g4025.t1.CDS3 | 29583294 | 29583411 |
| chr_3 | g4025 | g4025.t1 | exon | g4025.t1.exon4 | 29583569 | 29583748 |
| chr_3 | g4025 | g4025.t1 | cds | g4025.t1.CDS4 | 29583569 | 29583748 |
| chr_3 | g4025 | g4025.t1 | TSS | g4025.t1 | NA | NA |
| chr_3 | g4025 | g4025.t1 | TTS | g4025.t1 | NA | NA |
Sequences
>g4025.t1 Gene=g4025 Length=1650
ATGTCGTTTCATTTATTTTTAGATGAATTCGTTGCAGAAAATGGACTGCCAAGGCGCCTA
CGGACAGCATATACAAATACACAGCTGTTGGAGCTTGAAAAGGAATTTCATTTTAATAAA
TATTTATGTCGACCAAGAAGGATCGAAATTGCAGCGAGTCTTGATCTTACTGAACGTCAG
GTCAAAGTATGGTTTCAGAACAGGAGAATGAAATTTAAGCGACAAACACAATCAAAAACA
GACGATGAAGATTCAAGTAAAGACGACTTTAAGGGTGATGATGACACACAATCATGCAAT
TCTAACTCGAAAAAGTCATGTCAAGGTTGCGAATTGCCATCCGATGATGTACCCGACTCC
ACATCGAATTCACGCGGTCAAAACAATAATACGCCTAGTGCAACCAACAATAATCAATCA
AATATTAATGAACGAACAAATGGTGCAATTTCAAGAACAACTCCCAATTCGACAATTGAT
TTGGGAACACCGCAAAATAATACACAGAGTTTGATCTCCAATGCAGACTCTTCAATTGCA
TCTACAGGTAGTCTCGATGACGATGAATTAGAGACGCCTGTGAAAATTAAAAAGAAAGAT
GAAACGACGAGTGGAGGTCGAAAGAAAAAAGAGCCAAAAGCATCATCACAACATAATATG
TTTTCAAATAATGACGTCTATCGTAAGGAAAATGTGCAATCACCGCACGTAATTGCGAAA
GGCAATTTGAATTTTAATCGCGGCAACAACAACAATCAATATCAGAATCAGGTTAAAATA
AAGGGTCAACCAATAGTCGCAGCGATGCAGGAAGGTTACTTTCCTGGATTTTATGGAAAA
CATCCACCTCCGAATATTCACCATCAACCAAACGATGTCATGTTTGCAAAACACGAACTC
GAATTTCATCAGAAAGGTTTGTCAACACCTCAACAACAACAGCCACAAAATCAGCAATTT
CCACCATTTCATGGAGCTGCACAGAAGTATGAAATGCATGATTTTGAACATCAACTTAAA
AACGATAAAATGCCAATCGTCACAGGAGCTGGCATTCATGCTACACGTCCACCAATCGAT
TTTCCATCGCCACAAAATTCACAAATGTACTACAATGAAAATACAGCTCAGAATTCACAT
AATCAATATTATCCGAATGAATTCGACATTGGAAATGACGCTGCAAATGCTGTCAATGGA
AATGTTAGTGGTGGGAGTAGCGGCGGTGGCTATTTTGATCAAAAATCTCAAGCACATTAT
TACGATATGAATTATCATCATCATAGTGGCGGCAATGATTATTCTGACATGTATGCTGCC
GGTCCAGGAAATGCAGCAGCAATTGTAAATGAAAATTGTGAAAACTTTGCATCATTCCAA
CAGTATTATGATCATCATCCACAACAACAGCAGCAACAGCAGCAAAATATGCATGCACAT
CCACACCATTATCCGCCACATCATCATGTCGCACATCAACAAAATTTAACAAATCCAATT
GCCACAGCTTATGTTCATCATCAACAAAATTTTGCATCAAATGCACAAATTCATGGCACA
AATCTAACTGAAAATAGCAACAGTTCATCAGATTTTAATTTCTTGAGTAATTTAAATGAT
TTTGCGCCTGAATATTATCAATTGAGTTAG
>g4025.t1 Gene=g4025 Length=549
MSFHLFLDEFVAENGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQ
VKVWFQNRRMKFKRQTQSKTDDEDSSKDDFKGDDDTQSCNSNSKKSCQGCELPSDDVPDS
TSNSRGQNNNTPSATNNNQSNINERTNGAISRTTPNSTIDLGTPQNNTQSLISNADSSIA
STGSLDDDELETPVKIKKKDETTSGGRKKKEPKASSQHNMFSNNDVYRKENVQSPHVIAK
GNLNFNRGNNNNQYQNQVKIKGQPIVAAMQEGYFPGFYGKHPPPNIHHQPNDVMFAKHEL
EFHQKGLSTPQQQQPQNQQFPPFHGAAQKYEMHDFEHQLKNDKMPIVTGAGIHATRPPID
FPSPQNSQMYYNENTAQNSHNQYYPNEFDIGNDAANAVNGNVSGGSSGGGYFDQKSQAHY
YDMNYHHHSGGNDYSDMYAAGPGNAAAIVNENCENFASFQQYYDHHPQQQQQQQQNMHAH
PHHYPPHHHVAHQQNLTNPIATAYVHHQQNFASNAQIHGTNLTENSNSSSDFNFLSNLND
FAPEYYQLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4025.t1 | CDD | cd00086 | homeodomain | 18 | 75 | 4.84665E-25 |
| 8 | g4025.t1 | Gene3D | G3DSA:1.10.10.60 | - | 11 | 79 | 2.1E-28 |
| 16 | g4025.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 143 | - |
| 12 | g4025.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 95 | - |
| 15 | g4025.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 143 | - |
| 13 | g4025.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 182 | 223 | - |
| 14 | g4025.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 188 | 215 | - |
| 2 | g4025.t1 | PANTHER | PTHR45664 | PROTEIN ZERKNUELLT 1-RELATED | 11 | 492 | 8.4E-64 |
| 3 | g4025.t1 | PANTHER | PTHR45664:SF2 | HOMEOTIC PROTEIN PROBOSCIPEDIA | 11 | 492 | 8.4E-64 |
| 6 | g4025.t1 | PRINTS | PR00024 | Homeobox signature | 39 | 50 | 1.6E-7 |
| 4 | g4025.t1 | PRINTS | PR00024 | Homeobox signature | 54 | 64 | 1.6E-7 |
| 5 | g4025.t1 | PRINTS | PR00024 | Homeobox signature | 64 | 73 | 1.6E-7 |
| 1 | g4025.t1 | Pfam | PF00046 | Homeodomain | 18 | 74 | 1.4E-21 |
| 11 | g4025.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 50 | 73 | - |
| 17 | g4025.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 15 | 75 | 21.135 |
| 10 | g4025.t1 | SMART | SM00389 | HOX_1 | 17 | 79 | 2.2E-28 |
| 7 | g4025.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 13 | 75 | 4.15E-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: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 K09302 (homeobox protein HoxA/B2)
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