General information for g4057.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein abdominal-B.
Parent gene
- The parent gene g4057 is located on chr_3: 30252090..30272916 (- 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 | g4057 | g4057.t1 | isoform | g4057.t1 | 30246066 | 30272916 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon1 | 30246066 | 30246231 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS1 | 30246066 | 30246231 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon2 | 30246300 | 30246311 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS2 | 30246300 | 30246311 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon3 | 30246376 | 30246598 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS3 | 30246376 | 30246598 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon4 | 30247802 | 30247906 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS4 | 30247802 | 30247906 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon5 | 30251290 | 30251449 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS5 | 30251290 | 30251449 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon6 | 30251506 | 30251687 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS6 | 30251506 | 30251687 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon7 | 30251752 | 30252090 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS7 | 30251752 | 30252090 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon8 | 30258401 | 30258446 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS8 | 30258401 | 30258446 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon9 | 30260140 | 30260198 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS9 | 30260140 | 30260198 |
| chr_3 | g4057 | g4057.t1 | exon | g4057.t1.exon10 | 30272901 | 30272916 |
| chr_3 | g4057 | g4057.t1 | cds | g4057.t1.CDS10 | 30272901 | 30272916 |
| chr_3 | g4057 | g4057.t1 | TSS | g4057.t1 | NA | NA |
| chr_3 | g4057 | g4057.t1 | TTS | g4057.t1 | NA | NA |
Sequences
>g4057.t1 Gene=g4057 Length=1308
ATGATTGTTAAACGAGAAAGTAATGAAAGTTACTTTGGAGCTTATAAAATTGGTAGTACA
GTAATAATTCCCAAGCTCTTTAATCGCGGTCACACAAATCTGGCTAGTGCAGCAGCTTAC
GGGTCTCACGCTGCTGGGCCTTGGTGGGGGACTCAACCCCATCATCCACACCACCCACAC
GCCAGTGCTGCTATGTATGAGGACTCCACTGGTCAAAACACGACAACACATCACCACCAC
AGTCCGCCATTGTTATCAGTACACAATCCAAACGCATTGCTATCAGCACAAGTGCAACAG
CAACAACAACAGCAGCAATCATCAGCACAACCACCACTCACACCTCAACAAAACTCCCAA
ACGAACGGTACACACACAAACGGTACAGTGGCGTCTGCACAACCGCAACAAATCGTTACG
CCATCGGCGGCTAGCGATTCACCTGTTTCACCACCGACAGGACCACTCCATATACCAGCA
ATACCTGCAGCAAAACGACCAGGTTATGAAGACAGCTCATTATTGAGACAGCCATGGGGT
TATGATCCACCATTTGATTACAATTATCCAACCAGCTATCCATACTCTATCGAGCGAGAT
CGAAAAGTATTTTATTCTTCTTATCCTGATCAATATGCTCAACACTATTGGAATCGAGAA
CAACAATTTCCTGTGGAAGAAAAACCAATAATTACGCCAAGGCAAACAGAAACAACATCG
AGCGCTCAAAGCTCATATGAGAACACTTATACAAACAGTCTAAGATCTTATACATCTGAT
CCTGCTGGATATTCAACTACTGATCATATTAAGCGAGAAATTGATTTGAAACGATTATAT
GGTAAAAATTTAGAAAGCGATTATGAGTTTTTATCATCAAGACGATCTCTGTACAATGAT
TCGAAAGGTTCAACAATTACAGGATCTTCAGCAATTGGTTCAGCGACACCATCGAATCCA
TTAGAATGGCCAAATCAAGTTGTAACCGTCCGTAAAAAACGTAAACCTTATTCAAAATTT
CAGACATTGGAACTCGAGAAGGAATTTCTTTTTAATGCATATGTTTCAAAGCAAAAGCGA
TGGGAACTTGCTAGAAACTTGAATCTTACTGAGCGTCAAGTTAAAATTTGGTTCCAAAAT
AGACGAATGAAGAATAAAAAAAACTCGCAAAGACAGCAGGCAAATGCAAACAACGCAAAT
TCAAACAGTCATCATAATCACGTACCACCACAGACACACCATAACGCTCACCATATCGGT
TTGGGCTTAGGCATGCATCATCATCCACCGAAGATGCATCATCAGTGA
>g4057.t1 Gene=g4057 Length=435
MIVKRESNESYFGAYKIGSTVIIPKLFNRGHTNLASAAAYGSHAAGPWWGTQPHHPHHPH
ASAAMYEDSTGQNTTTHHHHSPPLLSVHNPNALLSAQVQQQQQQQQSSAQPPLTPQQNSQ
TNGTHTNGTVASAQPQQIVTPSAASDSPVSPPTGPLHIPAIPAAKRPGYEDSSLLRQPWG
YDPPFDYNYPTSYPYSIERDRKVFYSSYPDQYAQHYWNREQQFPVEEKPIITPRQTETTS
SAQSSYENTYTNSLRSYTSDPAGYSTTDHIKREIDLKRLYGKNLESDYEFLSSRRSLYND
SKGSTITGSSAIGSATPSNPLEWPNQVVTVRKKRKPYSKFQTLELEKEFLFNAYVSKQKR
WELARNLNLTERQVKIWFQNRRMKNKKNSQRQQANANNANSNSHHNHVPPQTHHNAHHIG
LGLGMHHHPPKMHHQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4057.t1 | CDD | cd00086 | homeodomain | 331 | 389 | 7.83971E-23 |
| 8 | g4057.t1 | Gene3D | G3DSA:1.10.10.60 | - | 298 | 390 | 6.9E-23 |
| 12 | g4057.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 123 | - |
| 13 | g4057.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 382 | 415 | - |
| 14 | g4057.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 389 | 409 | - |
| 2 | g4057.t1 | PANTHER | PTHR45970:SF2 | AGAP004664-PA | 301 | 409 | 7.7E-62 |
| 3 | g4057.t1 | PANTHER | PTHR45970 | AGAP004664-PA | 301 | 409 | 7.7E-62 |
| 4 | g4057.t1 | PRINTS | PR00024 | Homeobox signature | 352 | 363 | 5.9E-6 |
| 6 | g4057.t1 | PRINTS | PR00024 | Homeobox signature | 367 | 377 | 5.9E-6 |
| 5 | g4057.t1 | PRINTS | PR00024 | Homeobox signature | 377 | 386 | 5.9E-6 |
| 1 | g4057.t1 | Pfam | PF00046 | Homeodomain | 331 | 387 | 3.1E-19 |
| 11 | g4057.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 363 | 386 | - |
| 15 | g4057.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 328 | 388 | 20.293 |
| 10 | g4057.t1 | SMART | SM00389 | HOX_1 | 330 | 392 | 6.2E-23 |
| 7 | g4057.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 311 | 388 | 1.24E-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 K09300 (homeobox protein abdominal-B and related proteins)
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