General information for g5477.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeotic protein caudal.
Parent gene
- The parent gene g5477 is located on chr_2: 9796113..9801558 (- 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_2 | g5477 | g5477.t3 | TTS | g5477.t3 | 9795444 | 9795444 |
| chr_2 | g5477 | g5477.t3 | isoform | g5477.t3 | 9796113 | 9801558 |
| chr_2 | g5477 | g5477.t3 | exon | g5477.t3.exon1 | 9796113 | 9796439 |
| chr_2 | g5477 | g5477.t3 | cds | g5477.t3.CDS1 | 9796113 | 9796439 |
| chr_2 | g5477 | g5477.t3 | exon | g5477.t3.exon2 | 9796501 | 9796658 |
| chr_2 | g5477 | g5477.t3 | cds | g5477.t3.CDS2 | 9796501 | 9796658 |
| chr_2 | g5477 | g5477.t3 | exon | g5477.t3.exon3 | 9800507 | 9801558 |
| chr_2 | g5477 | g5477.t3 | cds | g5477.t3.CDS3 | 9800507 | 9800876 |
| chr_2 | g5477 | g5477.t3 | TSS | g5477.t3 | NA | NA |
Sequences
>g5477.t3 Gene=g5477 Length=1537
ATGGCGTTGTTCTTAGTTTCTATTGGCTACTCATATCTTGTTATAATGCCACGCCCACAA
GCTTCATGTAATAGTGCCGATTCGAAATATTTTTTTGTATGCCTGCATTCAATTGAAAAG
AACACGTCGTGTAGACAAGGCGAATTTCTTCGTAGTGGAAAATATTTATTTTTAAATAAG
AGAAAAATAAATAGAAAATAAAAGAAGTGATTCTTATTGTTATTATTTAAGTGATGAGAA
TGAAATATAAAGACAAATAAGCACTGATTTATATTGTGTTAAATAGTAGTAGATTTTATG
AGTCATTTGGCAATAGAGAGAAAGAAAAAAACAATCGAGTGATTAAGTAATTAATTAGAT
AGTCGATTAATAATTACAAACGCAAATAAAAAACTATTACACGTGAGAAAGGCAGTGCAT
ACTTGAACAAAATATAAAGAATAAATGCAGTGATTTTTCACAGCTCTTTTGTTATACGAC
TGTGATTATTTGAAAGTATTTTTGCTGAAAATATAAAAATGGTGTCTTATTATAATCATC
CGTTTGCGATGTATCAAAAGAATCACAACGGAAGTTCAAATTTAGCTTATTCTGCATCAC
CTTCTGCTTGGTATTCATCAAATTATCATCATCATCAGCCACAAATGCAGCTCAATTTCT
TGATACAGAACCAACACAACATATGTATCATTATCCACCTCATATGCTTCCTCCACAACC
TTCGCCTGATTGGGGACATGATAATTATGTTCCATCACCTCAAAATTCAGCACTCAGCAC
TGGCAGTGGTCCAGGTTCAGCTGCTTTTCTATCGTTAAATCAAGCAACAACAAATGGATC
ATCCATAAATGATCATCATCATCATATGAGTGACTCAATTCCAAATTTACCATCGCCACC
AGCCACAGTTCATTCAAATAGTGACATGAGTTCACCAGGCGCATGTGGACCATCTTCATC
ACCACAACAACAACTTAACTCACGACCGACGCCTGTCAAAAGTCCATACGAGTGGATGAA
AAAACCTTCATATCAGAGTCAACCAAATCCAGGAAAAACTCGAACAAAAGATAAATATCG
TGTGGTATATACAGACCATCAGCGACTTGAATTAGAGAAGGAATTTCATTTTACTCGATA
TATCACAATTCGTCGTAAAGCTGAATTAGCACAAACTCTTGCTCTTTCTGAAAGACAAGT
AAAAATATGGTTCCAAAACCGTCGCGCAAAAGATCGCAAACAAAAGAAGAAGATTGATTC
GGGCATTCCAATTTCAATGAATAGTCAAACAATTCTTTCACAATCACACATTAATAGCTC
ATCAACAATATCATCGAATTCACATCATTTACTTGATGTAAAACCAAAATTGGAACCATC
TTTGCATTTACAGCATTTGCATCAAATGAGTGCAATGGGTATGGGTATGTCACAAATGGG
ACTTCATCATGCACATTTGCATTCACTAGCACCAATGCCGTCAACACAGACACCTATTCC
GAATTCACAATCACCTTCACCGATGTTGATGAATTAA
>g5477.t3 Gene=g5477 Length=284
MYHYPPHMLPPQPSPDWGHDNYVPSPQNSALSTGSGPGSAAFLSLNQATTNGSSINDHHH
HMSDSIPNLPSPPATVHSNSDMSSPGACGPSSSPQQQLNSRPTPVKSPYEWMKKPSYQSQ
PNPGKTRTKDKYRVVYTDHQRLELEKEFHFTRYITIRRKAELAQTLALSERQVKIWFQNR
RAKDRKQKKKIDSGIPISMNSQTILSQSHINSSSTISSNSHHLLDVKPKLEPSLHLQHLH
QMSAMGMGMSQMGLHHAHLHSLAPMPSTQTPIPNSQSPSPMLMN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5477.t3 | CDD | cd00086 | homeodomain | 131 | 188 | 8.24121E-23 |
| 9 | g5477.t3 | Gene3D | G3DSA:1.10.10.60 | - | 103 | 189 | 8.5E-28 |
| 16 | g5477.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 38 | - |
| 13 | g5477.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 38 | - |
| 14 | g5477.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 131 | - |
| 15 | g5477.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 74 | 104 | - |
| 2 | g5477.t3 | PANTHER | PTHR24332 | HOMEOBOX PROTEIN CDX | 8 | 252 | 3.3E-49 |
| 4 | g5477.t3 | PRINTS | PR00024 | Homeobox signature | 151 | 162 | 4.7E-6 |
| 6 | g5477.t3 | PRINTS | PR00031 | Lambda-repressor HTH signature | 158 | 167 | 1.8E-5 |
| 5 | g5477.t3 | PRINTS | PR00024 | Homeobox signature | 166 | 176 | 4.7E-6 |
| 7 | g5477.t3 | PRINTS | PR00031 | Lambda-repressor HTH signature | 167 | 183 | 1.8E-5 |
| 3 | g5477.t3 | PRINTS | PR00024 | Homeobox signature | 176 | 185 | 4.7E-6 |
| 1 | g5477.t3 | Pfam | PF00046 | Homeodomain | 131 | 186 | 1.4E-19 |
| 12 | g5477.t3 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 162 | 185 | - |
| 17 | g5477.t3 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 127 | 187 | 20.293 |
| 11 | g5477.t3 | SMART | SM00389 | HOX_1 | 129 | 191 | 7.8E-24 |
| 8 | g5477.t3 | SUPERFAMILY | SSF46689 | Homeodomain-like | 111 | 189 | 5.99E-24 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5477/g5477.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5477.t3.fa.iupred3.txt does not exist
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 K09312 (homeobox protein CDX1/4)
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.
