General information for g4042.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeotic protein ultrabithorax.
Parent gene
- The parent gene g4042 is located on chr_3: 29995657..29998745 (- 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 | g4042 | g4042.t1 | isoform | g4042.t1 | 29995657 | 29998745 |
| chr_3 | g4042 | g4042.t1 | exon | g4042.t1.exon1 | 29995657 | 29995906 |
| chr_3 | g4042 | g4042.t1 | cds | g4042.t1.CDS1 | 29995657 | 29995906 |
| chr_3 | g4042 | g4042.t1 | exon | g4042.t1.exon2 | 29996225 | 29996243 |
| chr_3 | g4042 | g4042.t1 | cds | g4042.t1.CDS2 | 29996225 | 29996243 |
| chr_3 | g4042 | g4042.t1 | exon | g4042.t1.exon3 | 29998139 | 29998745 |
| chr_3 | g4042 | g4042.t1 | cds | g4042.t1.CDS3 | 29998139 | 29998745 |
| chr_3 | g4042 | g4042.t1 | TSS | g4042.t1 | 29999298 | 29999298 |
| chr_3 | g4042 | g4042.t1 | TTS | g4042.t1 | NA | NA |
Sequences
>g4042.t1 Gene=g4042 Length=876
ATGAATTCATACTTTGAACAATCTGGCTTTTATGGCCATCCACATCAAGCAGCAGCAGGA
ATGATGTCATCATCAGGTCATGATCAAACAACAGCAGCAGCAGCCGCTTACAGAGGATTT
CCTTTATCACTTGGAATGTCTCCGTATGCCAATCATCACCTTCATCAGACACGAACAGCT
CAGGATTCACCGTACGATGCAAGCATTACAGCAGCATGCAAGCAAATCTATGATGGAGCA
TACAATAAAGATTGCTCTAAAACAGTATCCGGTAATGGGACAGCAAATGGAACGTCCAAT
AGCGGCTCTGCAAGTGCTGGCAATAACAATACAACTGACACAAATGGCTACAAAGATGTC
TGGAATTCTACCGGCAATAATGGCTCACAAAATTCAGCACCTGTTCGTCCATCAGCCTGC
ACACCCGATTCACGAGTTGGTGGTTATATCGATGCATCAGGTGGATCACCAGTCAGTCGT
ACTGGTTCATCTGCAACGGGTGGCGCATGGAACTCAAATTGCACCATCGGCACAACCGGC
TCGCAATCATCGGCTTCAGCAAGTTTACATCAGAATCATACTTTTTATCCATGGATGGCT
ATTGCAGGTTTATTAATTCGATTCTGTTTAAATTGTGAAAATATTCTGATTCTTGGTGAT
TTTAATCACGAATTGAAATTAAGCAGTCCACTCGAGTCGTTTATGCTTCAATCTTTTGAC
ACAAGGCTATTCTCACCACGCGAATCGACAACAAATGCTCGAACAGTTATCGATGAAGTA
TTCGATCGAATTGAAGACTATAATATTGAAGTTTTTATCTATGAATCATATTCATCTCAT
CACAAACCATTAGTCATTCGAATACATGAATTATAA
>g4042.t1 Gene=g4042 Length=291
MNSYFEQSGFYGHPHQAAAGMMSSSGHDQTTAAAAAYRGFPLSLGMSPYANHHLHQTRTA
QDSPYDASITAACKQIYDGAYNKDCSKTVSGNGTANGTSNSGSASAGNNNTTDTNGYKDV
WNSTGNNGSQNSAPVRPSACTPDSRVGGYIDASGGSPVSRTGSSATGGAWNSNCTIGTTG
SQSSASASLHQNHTFYPWMAIAGLLIRFCLNCENILILGDFNHELKLSSPLESFMLQSFD
TRLFSPRESTTNARTVIDEVFDRIEDYNIEVFIYESYSSHHKPLVIRIHEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g4042.t1 | Coils | Coil | Coil | 288 | 291 | - |
| 1 | g4042.t1 | PANTHER | PTHR45659:SF15 | HOMEOTIC PROTEIN ULTRABITHORAX | 1 | 203 | 2.1E-47 |
| 2 | g4042.t1 | PANTHER | PTHR45659 | HOMEOBOX PROTEIN HOX | 1 | 203 | 2.1E-47 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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