General information for g7443.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Muscle segmentation homeobox.
Parent gene
- The parent gene g7443 is located on chr_2: 23715612..23716837 (+ 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 | g7443 | g7443.t1 | TSS | g7443.t1 | 23715378 | 23715378 |
| chr_2 | g7443 | g7443.t1 | isoform | g7443.t1 | 23715612 | 23716837 |
| chr_2 | g7443 | g7443.t1 | exon | g7443.t1.exon1 | 23715612 | 23716293 |
| chr_2 | g7443 | g7443.t1 | cds | g7443.t1.CDS1 | 23715612 | 23716293 |
| chr_2 | g7443 | g7443.t1 | exon | g7443.t1.exon2 | 23716379 | 23716590 |
| chr_2 | g7443 | g7443.t1 | cds | g7443.t1.CDS2 | 23716379 | 23716590 |
| chr_2 | g7443 | g7443.t1 | exon | g7443.t1.exon3 | 23716709 | 23716837 |
| chr_2 | g7443 | g7443.t1 | cds | g7443.t1.CDS3 | 23716709 | 23716837 |
| chr_2 | g7443 | g7443.t1 | TTS | g7443.t1 | 23716847 | 23716847 |
Sequences
>g7443.t1 Gene=g7443 Length=1023
ATGACTGTAACGCCCATTCGTACAATTACGATGACAAGTCCGACGGTAACTTCAGTGGAT
ATTAATAAGGAGACAAAGGCCTCAAAAATCAGTAATTTTAGTGTTGCCTCACTGTTGGCT
GACACGCGATCAAAGGCGCTGCCAACACAAGTGTTTAAAAATAATAATCATCACATTTTT
AATCACAATAATAATGATGAAATTTCATCGCTTATGCCTAAAAATTTGTCAGTTTCAAAG
ACTGATGCGTGCAACTTACCCAATTCAAATAATGATAATGACTGTAGTAGCAATTCTCTT
AACAATAAATTAAGTGACAGTGAAATAATTGAGAGAAAATCACATACACCTCATAGTTCT
ATTGCATCAGATGATTTCGATGAATCTTTACATGATGATGATGAAGAAGACTCAATTGTT
GATGTTGAGGATGTAAGAAATGAAAATAGTACAAACAGTAGCAATGTCGAATCACCTAAA
AGTGGCGATGCGATGCATGCTCATCAATTGGTTGCAGGACAGGCACTAATACGACCAACA
CCATTTAGTGCACTAGCAGCAGCTGCCGCAGCTTGGGGCATGAATAATGGTGTGCCTGGT
TGGCCAAATCGACAAATTCCACCGCCCTTCCGACCGCCAGAACTTTTTCCTGGTCAAGTA
CTGCCCGGTCAACTTAATGGAAATAATGAATTACCGCGTATTAAATGCAATTTGCGAAAA
CACAAACCAAACAGAAAACCGCGAACGCCATTTACAACGCAACAGCTTTTATCATTGGAA
AAGAAATTTCGTGAGAAACAGTATCTTAGCATAGCGGAACGTGCAGAATTTTCCTCATCA
TTGAGACTAACAGAAACACAAGTAAAAATCTGGTTCCAGAACAGGAGAGCTAAGGCTAAA
AGACTTCAGGAGGCTGAATTAGAGAAAATAAAAATGGCAGCATTAGGACGAGCACCAGGA
GCACAACTTTATATGGGATATTTTCATCCTACCCTCATAAATGAAGCAATGCATTTGCTT
TAA
>g7443.t1 Gene=g7443 Length=340
MTVTPIRTITMTSPTVTSVDINKETKASKISNFSVASLLADTRSKALPTQVFKNNNHHIF
NHNNNDEISSLMPKNLSVSKTDACNLPNSNNDNDCSSNSLNNKLSDSEIIERKSHTPHSS
IASDDFDESLHDDDEEDSIVDVEDVRNENSTNSSNVESPKSGDAMHAHQLVAGQALIRPT
PFSALAAAAAAWGMNNGVPGWPNRQIPPPFRPPELFPGQVLPGQLNGNNELPRIKCNLRK
HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLRLTETQVKIWFQNRRAKAK
RLQEAELEKIKMAALGRAPGAQLYMGYFHPTLINEAMHLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7443.t1 | CDD | cd00086 | homeodomain | 245 | 303 | 2.24899E-21 |
| 8 | g7443.t1 | Gene3D | G3DSA:1.10.10.60 | - | 224 | 306 | 3.9E-23 |
| 13 | g7443.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 112 | 163 | - |
| 14 | g7443.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 112 | 126 | - |
| 12 | g7443.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 127 | 142 | - |
| 15 | g7443.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 145 | 160 | - |
| 2 | g7443.t1 | PANTHER | PTHR24338:SF0 | MUSCLE SEGMENTATION HOMEOBOX | 15 | 333 | 5.4E-82 |
| 3 | g7443.t1 | PANTHER | PTHR24338 | HOMEOBOX PROTEIN MSX | 15 | 333 | 5.4E-82 |
| 6 | g7443.t1 | PRINTS | PR00024 | Homeobox signature | 266 | 277 | 3.3E-6 |
| 4 | g7443.t1 | PRINTS | PR00024 | Homeobox signature | 281 | 291 | 3.3E-6 |
| 5 | g7443.t1 | PRINTS | PR00024 | Homeobox signature | 291 | 300 | 3.3E-6 |
| 1 | g7443.t1 | Pfam | PF00046 | Homeodomain | 245 | 301 | 1.3E-20 |
| 11 | g7443.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 277 | 300 | - |
| 16 | g7443.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 242 | 302 | 20.423 |
| 10 | g7443.t1 | SMART | SM00389 | HOX_1 | 244 | 306 | 1.2E-23 |
| 7 | g7443.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 236 | 303 | 2.18E-22 |
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 K09341 (homeobox protein MSX)
Pathway
- This transcript belongs to the following 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