General information for g1945.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Myogenic-determination protein.
Parent gene
- The parent gene g1945 is located on chr_3: 14003798..14008648 (- 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 | g1945 | g1945.t1 | TTS | g1945.t1 | 14003201 | 14003201 |
| chr_3 | g1945 | g1945.t1 | isoform | g1945.t1 | 14003798 | 14008648 |
| chr_3 | g1945 | g1945.t1 | exon | g1945.t1.exon1 | 14003798 | 14004027 |
| chr_3 | g1945 | g1945.t1 | cds | g1945.t1.CDS1 | 14003798 | 14004027 |
| chr_3 | g1945 | g1945.t1 | exon | g1945.t1.exon2 | 14004101 | 14004179 |
| chr_3 | g1945 | g1945.t1 | cds | g1945.t1.CDS2 | 14004101 | 14004179 |
| chr_3 | g1945 | g1945.t1 | exon | g1945.t1.exon3 | 14007974 | 14008051 |
| chr_3 | g1945 | g1945.t1 | cds | g1945.t1.CDS3 | 14007974 | 14008051 |
| chr_3 | g1945 | g1945.t1 | exon | g1945.t1.exon4 | 14008109 | 14008231 |
| chr_3 | g1945 | g1945.t1 | cds | g1945.t1.CDS4 | 14008109 | 14008231 |
| chr_3 | g1945 | g1945.t1 | exon | g1945.t1.exon5 | 14008292 | 14008648 |
| chr_3 | g1945 | g1945.t1 | cds | g1945.t1.CDS5 | 14008292 | 14008648 |
| chr_3 | g1945 | g1945.t1 | TSS | g1945.t1 | 14008757 | 14008757 |
Sequences
>g1945.t1 Gene=g1945 Length=867
ATGACAAAATATAATCAGTGTATTAATACTAATCGAAAAGATCAAACAATAAACAACAAT
AAAAGTGAAAAGAACAAAATGAACTTCGACAGTGCTCGTGATTTTAATGATAATCTCGCG
ACAATGTTAGAAAGCAAAATGAATGGATTAATGGCTCATCAGCTTGACATGATTGACGAT
AGTAGTAGCATGAGTTCAATTGCGTCAACTGAAACTGAGCACGTTTTAGCGCCAAAGTGT
ATGGCTGGCAAAATGCAACCGTGTTTAACTTGGGCTTGTAAAGCATGTAAGAAAAAAAGT
GTCGCAGTTGATCGAAGAAGAGCAGCAACCATGAGAGAACGAAGAAGACTGAGAAAGGTT
AATGAAGCTTTTGAACTTTTAAAGAGAAGAACAAGTACAAATCCCAACCAAAGATTGCCA
AAAGTTGAAATTTTAAGAAATGCCATTGAATATATTGAATCACTTGAAGATTTATTACAG
GATACACCACAACCATTAAGACCAAGTCCAGACTTTAGTGACATGTCAAATGGACGACCA
ACAGTGCAAGATTATATGAACTGCTATGCTGGAAACTACCTCAAAGAACGTCTTTCACAT
CTGGGCAAGGACAGTGAAAAATTTACTCCAATTACAACATTTAATTTTAACTCACCAGTT
AATGGCTCAAGTCTTGATTGCCTCAATTTAATAGTGCAAAGCATAAATTCACCAGATTCC
AACGATATATTGAGCTCTCCAAATGCTTCAATTACTCATATACAACAGCAGCAGCAGCAA
CCTAATCAATCTACCGTGCAACTTCATCAAAATCATAACAACAACAGTAGCAGTAATTTA
AAGTGTGAATACGATGCTAAAGTGTAA
>g1945.t1 Gene=g1945 Length=288
MTKYNQCINTNRKDQTINNNKSEKNKMNFDSARDFNDNLATMLESKMNGLMAHQLDMIDD
SSSMSSIASTETEHVLAPKCMAGKMQPCLTWACKACKKKSVAVDRRRAATMRERRRLRKV
NEAFELLKRRTSTNPNQRLPKVEILRNAIEYIESLEDLLQDTPQPLRPSPDFSDMSNGRP
TVQDYMNCYAGNYLKERLSHLGKDSEKFTPITTFNFNSPVNGSSLDCLNLIVQSINSPDS
NDILSSPNASITHIQQQQQQPNQSTVQLHQNHNNNSSSNLKCEYDAKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1945.t1 | CDD | cd19699 | bHLH_TS_dMYOD_like | 104 | 159 | 0.0000000 |
| 8 | g1945.t1 | Gene3D | G3DSA:4.10.280.10 | HLH | 94 | 161 | 0.0000000 |
| 3 | g1945.t1 | PANTHER | PTHR11534 | MYOGENIC FACTOR | 5 | 236 | 0.0000000 |
| 4 | g1945.t1 | PANTHER | PTHR11534:SF9 | MYOGENIC-DETERMINATION PROTEIN | 5 | 236 | 0.0000000 |
| 2 | g1945.t1 | Pfam | PF01586 | Myogenic Basic domain | 57 | 104 | 0.0000000 |
| 1 | g1945.t1 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 105 | 156 | 0.0000000 |
| 9 | g1945.t1 | ProSiteProfiles | PS50888 | Myc-type, basic helix-loop-helix (bHLH) domain profile. | 104 | 155 | 15.8590000 |
| 7 | g1945.t1 | SMART | SM00520 | basic | 27 | 109 | 0.0000002 |
| 6 | g1945.t1 | SMART | SM00353 | finulus | 110 | 161 | 0.0000000 |
| 5 | g1945.t1 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 104 | 164 | 0.0000000 |
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:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0007517 | muscle organ development | BP |
| GO:0046983 | protein dimerization activity | MF |
KEGG
Orthology
- This transcript has been annotated with K18484 (myogenic factor 5)
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