General information for g4054.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeobox protein abdominal-A-like protein.
Parent gene
- The parent gene g4054 is located on chr_3: 30095629..30117151 (- 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 | g4054 | g4054.t1 | TTS | g4054.t1 | 30095535 | 30095535 |
| chr_3 | g4054 | g4054.t1 | isoform | g4054.t1 | 30095629 | 30117151 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon1 | 30095629 | 30095991 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS1 | 30095629 | 30095991 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon2 | 30096122 | 30096185 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS2 | 30096122 | 30096185 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon3 | 30097728 | 30097887 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS3 | 30097728 | 30097887 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon4 | 30109438 | 30109485 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS4 | 30109438 | 30109485 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon5 | 30114564 | 30114784 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS5 | 30114564 | 30114784 |
| chr_3 | g4054 | g4054.t1 | exon | g4054.t1.exon6 | 30116850 | 30117151 |
| chr_3 | g4054 | g4054.t1 | cds | g4054.t1.CDS6 | 30116850 | 30117151 |
| chr_3 | g4054 | g4054.t1 | TSS | g4054.t1 | NA | NA |
Sequences
>g4054.t1 Gene=g4054 Length=1158
ATGTCTAACGCCGCAATTTCATCATCAAAATTCATAATTGACACGATGCTACCAAAATAT
GCAAGTCAATTTCAACCATTTATCAATTCACATCTCATGAATAATCAGACATCAAATACA
AATTCAAATTCAACAGTGTCACAAACCCCAAATAATTCTGAAGGTAGTCCATTAACTGGT
AGTGAAGAAGGTAGTTCACCGCCGACTAATAAAATGTATCCATTTGTATCAAATCATCCG
ACGACACATTCGAGCTATCCAGCGATGCCTGGCTTCACTGGCTTAGATGATAAATCATGC
GGTCGATATTCAGAAAGCGTCATGAATAGTTATCCGTCAATGGGCAGTGCCTCGAGCATT
GCACAATTTTATCATCAAGCAGCGGCAGTTTCAGCGGCAGGCGCCGTTGGCATGGATTCG
CTTGGTAGTGCATGCTCGCAACTTTCATCTGGTGGTTTATCATCAGTTGGCACTGGACAA
GCACTCTCGGAAATCACTCGACATCCATGGCTCGTACCGACTGATTGGATGAGCAATCCC
TTCGATCGCGTTGTTTGCGGAGATTTTGCAGGACCCAATGGTTGTCCAAGAAGACGCGGT
CGTCAAACATACACACGCTTCCAGACATTGGAACTAGAAAAAGAGTTTCATTTTAATCAT
TATCTCACACGCAGAAGACGTATCGAAATTGCACATGCGTTATGTCTCACAGAGCGACAA
ATTAAAATTTGGTTCCAAAATCGCCGCATGAAATTAAAAAAAGAATTGCGTGCTGTTAAA
GAGATCAATGAGCAGGCAAGACGTGAAAGAGAAGAGCAAGAAAAAATGAAGCAAGAGACT
TTAAAGTCATCACAGCAGCAGCAACATCATCACAATAAGCATCAGCAACAGTCGCAGGAT
CATTCTGCACTCCTCTCATCACAGAACTCGCATGGCGGACAAGGTGGACCTCATAGTGGA
CATCTCGGTAATCACGGTGTTGGAGGTCTAGTTGGCAGTCATTTGCATCATCCATCGCTA
GTACAAAATGATTTGAAATTAGGTTTAGGTGGTATGGGCGGCGGTATTGGTGGTGGTTTG
GGAAATCTCGGCATGATGGGTCAGTTGGACAACAAAAATCAAGACATCTTAAAGGCAGTT
AGCAAAGTCAGCTCATAA
>g4054.t1 Gene=g4054 Length=385
MSNAAISSSKFIIDTMLPKYASQFQPFINSHLMNNQTSNTNSNSTVSQTPNNSEGSPLTG
SEEGSSPPTNKMYPFVSNHPTTHSSYPAMPGFTGLDDKSCGRYSESVMNSYPSMGSASSI
AQFYHQAAAVSAAGAVGMDSLGSACSQLSSGGLSSVGTGQALSEITRHPWLVPTDWMSNP
FDRVVCGDFAGPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQ
IKIWFQNRRMKLKKELRAVKEINEQARREREEQEKMKQETLKSSQQQQHHHNKHQQQSQD
HSALLSSQNSHGGQGGPHSGHLGNHGVGGLVGSHLHHPSLVQNDLKLGLGGMGGGIGGGL
GNLGMMGQLDNKNQDILKAVSKVSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4054.t1 | CDD | cd00086 | homeodomain | 198 | 255 | 4.22358E-24 |
| 10 | g4054.t1 | Coils | Coil | Coil | 249 | 288 | - |
| 9 | g4054.t1 | Gene3D | G3DSA:1.10.10.60 | - | 174 | 258 | 6.6E-29 |
| 16 | g4054.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 67 | - |
| 15 | g4054.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 266 | 318 | - |
| 14 | g4054.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 298 | 315 | - |
| 3 | g4054.t1 | PANTHER | PTHR45659:SF8 | HOMEOBOX PROTEIN ABDOMINAL-A-RELATED | 113 | 325 | 1.2E-82 |
| 4 | g4054.t1 | PANTHER | PTHR45659 | HOMEOBOX PROTEIN HOX | 113 | 325 | 1.2E-82 |
| 7 | g4054.t1 | PRINTS | PR00024 | Homeobox signature | 219 | 230 | 1.0E-7 |
| 6 | g4054.t1 | PRINTS | PR00024 | Homeobox signature | 234 | 244 | 1.0E-7 |
| 5 | g4054.t1 | PRINTS | PR00024 | Homeobox signature | 244 | 253 | 1.0E-7 |
| 2 | g4054.t1 | Pfam | PF00046 | Homeodomain | 198 | 254 | 6.9E-20 |
| 1 | g4054.t1 | Pfam | PF12407 | Homeobox protein | 255 | 277 | 3.5E-12 |
| 13 | g4054.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 230 | 253 | - |
| 17 | g4054.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 195 | 255 | 20.504 |
| 12 | g4054.t1 | SMART | SM00389 | HOX_1 | 197 | 259 | 1.6E-23 |
| 8 | g4054.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 174 | 255 | 2.44E-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: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 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