General information for g5476.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 g5476 is located on chr_2: 9790101..9794973 (+ 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 | g5476 | g5476.t1 | TSS | g5476.t1 | 9789691 | 9789691 |
| chr_2 | g5476 | g5476.t1 | isoform | g5476.t1 | 9790101 | 9794804 |
| chr_2 | g5476 | g5476.t1 | exon | g5476.t1.exon1 | 9790101 | 9790371 |
| chr_2 | g5476 | g5476.t1 | cds | g5476.t1.CDS1 | 9790101 | 9790371 |
| chr_2 | g5476 | g5476.t1 | exon | g5476.t1.exon2 | 9790454 | 9790681 |
| chr_2 | g5476 | g5476.t1 | cds | g5476.t1.CDS2 | 9790454 | 9790681 |
| chr_2 | g5476 | g5476.t1 | exon | g5476.t1.exon3 | 9794403 | 9794560 |
| chr_2 | g5476 | g5476.t1 | cds | g5476.t1.CDS3 | 9794403 | 9794560 |
| chr_2 | g5476 | g5476.t1 | exon | g5476.t1.exon4 | 9794625 | 9794804 |
| chr_2 | g5476 | g5476.t1 | cds | g5476.t1.CDS4 | 9794625 | 9794804 |
| chr_2 | g5476 | g5476.t1 | TTS | g5476.t1 | 9794961 | 9794961 |
Sequences
>g5476.t1 Gene=g5476 Length=837
ATGGTGTCTTATTATAATCATCCGTTTGCGATGTATCAAAAGAATCACAACGGAAGTTCA
AATTTAGCTTATTCTGCATCACCTTCTGCTTGGTATTCATCAAATTATCATCATCATCAG
CCACCAAATGCAGCTCAATTTCTTGATACAGAACCAACACAACATATGTATCATTATCCA
CCTCATATGCTTCCTCCACAACCTTCGCCTGATTGGGGACATGATAATTATGTTCCATCA
CCTCAAAATTCAGCACTCAGCACTGGCAGTGCAACAACAAATGGATCATCCAATAATGAT
CATCATCATCATATGAGTGACTCAATTCCAAATTTACCATCGCCACCAGCCACAGTTCAT
TCAAATAGTGACATGAGTTCACCAGGCGCATGTGGACCATCTTCATCACCACAACAACAA
CTTAACTCACGACCGACGCCTGTCAAAAGTCCATACGAGTGGATGAAAAAACCTTCATAT
CAGAGTCAACCAAATCCAGGAAAAACTCGAACAAAAGACAAATATCGCGTGGTTTATACA
GATCATCAGCGTTTAGAGCTAGAGAAAGAGTATCATTACACTCGTTATATTACAATCAGA
AGAAAATCAGAACTTTCTCAGACGTTAGGACTTTCAGAGAGACAAGTAAAAATATGGTTC
CAAAATCGTCGAGCAAAAGATCGCAAGACTAAGAAGAAGCTTGAATTTGGTATTGTTCCA
ACATCTTCAACATCATCAAATAGTAACATATCATCATTATTGGATGTGAAACCAAAAATT
GATCCAATTCATCTTCAGCATCTGCAAATGAATGCATTTGGTTTAAGACTTCGATAA
>g5476.t1 Gene=g5476 Length=278
MVSYYNHPFAMYQKNHNGSSNLAYSASPSAWYSSNYHHHQPPNAAQFLDTEPTQHMYHYP
PHMLPPQPSPDWGHDNYVPSPQNSALSTGSATTNGSSNNDHHHHMSDSIPNLPSPPATVH
SNSDMSSPGACGPSSSPQQQLNSRPTPVKSPYEWMKKPSYQSQPNPGKTRTKDKYRVVYT
DHQRLELEKEYHYTRYITIRRKSELSQTLGLSERQVKIWFQNRRAKDRKTKKKLEFGIVP
TSSTSSNSNISSLLDVKPKIDPIHLQHLQMNAFGLRLR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5476.t1 | CDD | cd00086 | homeodomain | 174 | 231 | 5.99194E-22 |
| 10 | g5476.t1 | Gene3D | G3DSA:1.10.10.60 | - | 146 | 232 | 9.4E-27 |
| 15 | g5476.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 174 | - |
| 16 | g5476.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 99 | - |
| 14 | g5476.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 147 | - |
| 2 | g5476.t1 | PANTHER | PTHR24332:SF16 | HOMEOBOX PROTEIN CDX-1 | 10 | 245 | 4.9E-51 |
| 3 | g5476.t1 | PANTHER | PTHR24332 | HOMEOBOX PROTEIN CDX | 10 | 245 | 4.9E-51 |
| 6 | g5476.t1 | PRINTS | PR00024 | Homeobox signature | 194 | 205 | 4.3E-6 |
| 7 | g5476.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 201 | 210 | 4.7E-7 |
| 4 | g5476.t1 | PRINTS | PR00024 | Homeobox signature | 209 | 219 | 4.3E-6 |
| 8 | g5476.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 210 | 226 | 4.7E-7 |
| 5 | g5476.t1 | PRINTS | PR00024 | Homeobox signature | 219 | 228 | 4.3E-6 |
| 1 | g5476.t1 | Pfam | PF00046 | Homeodomain | 174 | 229 | 8.3E-20 |
| 13 | g5476.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 205 | 228 | - |
| 17 | g5476.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 170 | 230 | 19.742 |
| 12 | g5476.t1 | SMART | SM00389 | HOX_1 | 172 | 234 | 2.2E-24 |
| 9 | g5476.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 154 | 232 | 2.01E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5476/g5476.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5476.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.
