General information for g5477.t1
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.t1 | TTS | g5477.t1 | 9795444 | 9795444 |
| chr_2 | g5477 | g5477.t1 | isoform | g5477.t1 | 9796113 | 9801558 |
| chr_2 | g5477 | g5477.t1 | exon | g5477.t1.exon1 | 9796113 | 9796439 |
| chr_2 | g5477 | g5477.t1 | cds | g5477.t1.CDS1 | 9796113 | 9796439 |
| chr_2 | g5477 | g5477.t1 | exon | g5477.t1.exon2 | 9796501 | 9796658 |
| chr_2 | g5477 | g5477.t1 | cds | g5477.t1.CDS2 | 9796501 | 9796658 |
| chr_2 | g5477 | g5477.t1 | exon | g5477.t1.exon3 | 9800507 | 9800920 |
| chr_2 | g5477 | g5477.t1 | cds | g5477.t1.CDS3 | 9800507 | 9800920 |
| chr_2 | g5477 | g5477.t1 | exon | g5477.t1.exon4 | 9801492 | 9801558 |
| chr_2 | g5477 | g5477.t1 | cds | g5477.t1.CDS4 | 9801492 | 9801558 |
| chr_2 | g5477 | g5477.t1 | TSS | g5477.t1 | NA | NA |
Sequences
>g5477.t1 Gene=g5477 Length=966
ATGGCGTTGTTCTTAGTTTCTATTGGCTACTCATATCTTGTTATAATGCCACGCCCACAA
GCTTCATCCACAAATGCAGCTCAATTTCTTGATACAGAACCAACACAACATATGTATCAT
TATCCACCTCATATGCTTCCTCCACAACCTTCGCCTGATTGGGGACATGATAATTATGTT
CCATCACCTCAAAATTCAGCACTCAGCACTGGCAGTGGTCCAGGTTCAGCTGCTTTTCTA
TCGTTAAATCAAGCAACAACAAATGGATCATCCATAAATGATCATCATCATCATATGAGT
GACTCAATTCCAAATTTACCATCGCCACCAGCCACAGTTCATTCAAATAGTGACATGAGT
TCACCAGGCGCATGTGGACCATCTTCATCACCACAACAACAACTTAACTCACGACCGACG
CCTGTCAAAAGTCCATACGAGTGGATGAAAAAACCTTCATATCAGAGTCAACCAAATCCA
GGAAAAACTCGAACAAAAGATAAATATCGTGTGGTATATACAGACCATCAGCGACTTGAA
TTAGAGAAGGAATTTCATTTTACTCGATATATCACAATTCGTCGTAAAGCTGAATTAGCA
CAAACTCTTGCTCTTTCTGAAAGACAAGTAAAAATATGGTTCCAAAACCGTCGCGCAAAA
GATCGCAAACAAAAGAAGAAGATTGATTCGGGCATTCCAATTTCAATGAATAGTCAAACA
ATTCTTTCACAATCACACATTAATAGCTCATCAACAATATCATCGAATTCACATCATTTA
CTTGATGTAAAACCAAAATTGGAACCATCTTTGCATTTACAGCATTTGCATCAAATGAGT
GCAATGGGTATGGGTATGTCACAAATGGGACTTCATCATGCACATTTGCATTCACTAGCA
CCAATGCCGTCAACACAGACACCTATTCCGAATTCACAATCACCTTCACCGATGTTGATG
AATTAA
>g5477.t1 Gene=g5477 Length=321
MALFLVSIGYSYLVIMPRPQASSTNAAQFLDTEPTQHMYHYPPHMLPPQPSPDWGHDNYV
PSPQNSALSTGSGPGSAAFLSLNQATTNGSSINDHHHHMSDSIPNLPSPPATVHSNSDMS
SPGACGPSSSPQQQLNSRPTPVKSPYEWMKKPSYQSQPNPGKTRTKDKYRVVYTDHQRLE
LEKEFHFTRYITIRRKAELAQTLALSERQVKIWFQNRRAKDRKQKKKIDSGIPISMNSQT
ILSQSHINSSSTISSNSHHLLDVKPKLEPSLHLQHLHQMSAMGMGMSQMGLHHAHLHSLA
PMPSTQTPIPNSQSPSPMLMN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5477.t1 | CDD | cd00086 | homeodomain | 168 | 225 | 7.36036E-23 |
| 10 | g5477.t1 | Gene3D | G3DSA:1.10.10.60 | - | 140 | 226 | 1.1E-27 |
| 19 | g5477.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 141 | - |
| 20 | g5477.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 169 | - |
| 2 | g5477.t1 | PANTHER | PTHR24332 | HOMEOBOX PROTEIN CDX | 18 | 289 | 7.5E-50 |
| 4 | g5477.t1 | PRINTS | PR00024 | Homeobox signature | 188 | 199 | 6.3E-6 |
| 7 | g5477.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 195 | 204 | 2.2E-5 |
| 5 | g5477.t1 | PRINTS | PR00024 | Homeobox signature | 203 | 213 | 6.3E-6 |
| 6 | g5477.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 204 | 220 | 2.2E-5 |
| 3 | g5477.t1 | PRINTS | PR00024 | Homeobox signature | 213 | 222 | 6.3E-6 |
| 1 | g5477.t1 | Pfam | PF00046 | Homeodomain | 168 | 223 | 1.7E-19 |
| 12 | g5477.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 13 | g5477.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g5477.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 15 | g5477.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 26 | - |
| 11 | g5477.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 321 | - |
| 18 | g5477.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 199 | 222 | - |
| 21 | g5477.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 164 | 224 | 20.293 |
| 17 | g5477.t1 | SMART | SM00389 | HOX_1 | 166 | 228 | 7.8E-24 |
| 8 | g5477.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 148 | 226 | 7.7E-24 |
| 9 | g5477.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5477/g5477.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5477.t1.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. There were no conditions that were differentially expressed