General information for g4027.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein Hox-A3a.
Parent gene
- The parent gene g4027 is located on chr_3: 29621021..29623403 (- 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 | g4027 | g4027.t1 | isoform | g4027.t1 | 29621021 | 29623403 |
| chr_3 | g4027 | g4027.t1 | exon | g4027.t1.exon1 | 29621021 | 29621750 |
| chr_3 | g4027 | g4027.t1 | cds | g4027.t1.CDS1 | 29621021 | 29621750 |
| chr_3 | g4027 | g4027.t1 | exon | g4027.t1.exon2 | 29621888 | 29622056 |
| chr_3 | g4027 | g4027.t1 | cds | g4027.t1.CDS2 | 29621888 | 29622056 |
| chr_3 | g4027 | g4027.t1 | exon | g4027.t1.exon3 | 29623211 | 29623403 |
| chr_3 | g4027 | g4027.t1 | cds | g4027.t1.CDS3 | 29623211 | 29623403 |
| chr_3 | g4027 | g4027.t1 | TSS | g4027.t1 | NA | NA |
| chr_3 | g4027 | g4027.t1 | TTS | g4027.t1 | NA | NA |
Sequences
>g4027.t1 Gene=g4027 Length=1092
ATGATGCTTGAAAATCAAAATTTTTCAAATTGTGATTACAATTATGAACTACTGGACACA
AATTTGCCAGCAATTGAAAAATTAACAAGTGCAACAAGTGCAAATCATTCAACATTTAAG
TATTGGAATCCAGCAACAGATGATAATGATCATTTCGATTCAAATATTACGAAATTCAAT
AATGTTACTAAAGACTCAAAAACCGCTGATGCAATTATTCAAAAAAGATCAAGAACTGCA
TACACTTCAGTTCAGCTGATTGAACTTGAAAAAGAATTTAATATAAATAAATATTTATGT
CGTCCAAGGAGAATTGATTTGGCAAATCGTTTGCAATTAACTGAAAGACAGATTAAAATA
TGGTTCCAAAATCGTCGTATGAAATTCAAAAAAGACAACAGCAACATTAAATCAGTTAAT
AGATCATCGCCGTCATCACCAAGCAATCATTCTGATTCACTAAAATCAACACAATCATCA
ATTGACCGCAAGACAGACGATTGTCATCAGAAAATTGTAAAGAGATTAATGTCACATTCA
GCATCAATTAAAATTGAAGGCAGTTCATCGCCACCAAATCAAAATAATGTCGCACAAGTG
ACATCATCATCTTATGCACCTTATACAGTCTCTCACTATCCACAGACAGCTTACAATTAT
CATCATCAGATTTATAACAATATCAACAATAATAATATCATGATGAATGATTACTATTGC
TATCAACCAACACAACAAGAGCTACTGCCACAATTTGATTCTTTTCCATATGACACAACA
CCACCATTAACAACTTTCGATCAAAGCAGCAATGATTATATTTTCAATGGTGATTTTAGT
GTAAATTTTAATGGTTCCGATTTTGATGCTTCATTTCCGCTCATTGATGGTTTTAACTAT
CAAAAATCAACTGACAATCAAACATCAGTAGAAATCAAGCAATTATCACCGATCAAAATT
CAATCATTTGATGATGATGATGATGAAAAGAAATTTTACAGTGATGGTCAATCGATAGAA
TCTGAAACATCTGTTGCTACTTTAAATAATTGGAAATTTAATAATGAACCACAAATGGCA
GCATCGTATTAA
>g4027.t1 Gene=g4027 Length=363
MMLENQNFSNCDYNYELLDTNLPAIEKLTSATSANHSTFKYWNPATDDNDHFDSNITKFN
NVTKDSKTADAIIQKRSRTAYTSVQLIELEKEFNINKYLCRPRRIDLANRLQLTERQIKI
WFQNRRMKFKKDNSNIKSVNRSSPSSPSNHSDSLKSTQSSIDRKTDDCHQKIVKRLMSHS
ASIKIEGSSSPPNQNNVAQVTSSSYAPYTVSHYPQTAYNYHHQIYNNINNNNIMMNDYYC
YQPTQQELLPQFDSFPYDTTPPLTTFDQSSNDYIFNGDFSVNFNGSDFDASFPLIDGFNY
QKSTDNQTSVEIKQLSPIKIQSFDDDDDEKKFYSDGQSIESETSVATLNNWKFNNEPQMA
ASY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4027.t1 | CDD | cd00086 | homeodomain | 75 | 133 | 1.31582E-22 |
| 8 | g4027.t1 | Gene3D | G3DSA:1.10.10.60 | - | 30 | 136 | 3.2E-27 |
| 12 | g4027.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 165 | - |
| 13 | g4027.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 156 | - |
| 2 | g4027.t1 | PANTHER | PTHR45664:SF14 | PROTEIN ZERKNUELLT 1-RELATED | 30 | 257 | 3.3E-49 |
| 3 | g4027.t1 | PANTHER | PTHR45664 | PROTEIN ZERKNUELLT 1-RELATED | 30 | 257 | 3.3E-49 |
| 4 | g4027.t1 | PRINTS | PR00024 | Homeobox signature | 96 | 107 | 1.6E-7 |
| 6 | g4027.t1 | PRINTS | PR00024 | Homeobox signature | 111 | 121 | 1.6E-7 |
| 5 | g4027.t1 | PRINTS | PR00024 | Homeobox signature | 121 | 130 | 1.6E-7 |
| 1 | g4027.t1 | Pfam | PF00046 | Homeodomain | 75 | 131 | 5.6E-21 |
| 11 | g4027.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 107 | 130 | - |
| 14 | g4027.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 72 | 132 | 20.423 |
| 10 | g4027.t1 | SMART | SM00389 | HOX_1 | 74 | 136 | 1.2E-25 |
| 7 | g4027.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 73 | 132 | 1.2E-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 K09303 (homeobox protein HoxA/B/D3)
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