General information for g3978.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myosin heavy chain 95F.
Parent gene
- The parent gene g3978 is located on chr_3: 29354185..29355636 (+ 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 | g3978 | g3978.t4 | isoform | g3978.t4 | 29354185 | 29355636 |
| chr_3 | g3978 | g3978.t4 | exon | g3978.t4.exon1 | 29354185 | 29354411 |
| chr_3 | g3978 | g3978.t4 | cds | g3978.t4.CDS1 | 29354191 | 29354411 |
| chr_3 | g3978 | g3978.t4 | exon | g3978.t4.exon2 | 29354603 | 29354647 |
| chr_3 | g3978 | g3978.t4 | cds | g3978.t4.CDS2 | 29354603 | 29354647 |
| chr_3 | g3978 | g3978.t4 | exon | g3978.t4.exon3 | 29354888 | 29355126 |
| chr_3 | g3978 | g3978.t4 | cds | g3978.t4.CDS3 | 29354888 | 29355126 |
| chr_3 | g3978 | g3978.t4 | exon | g3978.t4.exon4 | 29355192 | 29355518 |
| chr_3 | g3978 | g3978.t4 | cds | g3978.t4.CDS4 | 29355192 | 29355518 |
| chr_3 | g3978 | g3978.t4 | exon | g3978.t4.exon5 | 29355602 | 29355636 |
| chr_3 | g3978 | g3978.t4 | cds | g3978.t4.CDS5 | 29355602 | 29355636 |
| chr_3 | g3978 | g3978.t4 | TSS | g3978.t4 | NA | NA |
| chr_3 | g3978 | g3978.t4 | TTS | g3978.t4 | NA | NA |
Sequences
>g3978.t4 Gene=g3978 Length=873
GCCGAAATGGAATTACGTAGAAAACAAGAAGAAGCCGAACGATTACGTCTCGAGGAAGAA
GACAGAAGAGCGGCTTTGCTACTTCAAGCGCAATTGGAAAAAGAGGCACAAGAAGATAGC
AAGTATCGCCAACAACTAGAGCAAGAGAGGCGTGACCATGAGTTAGCATTGCGTTTAGCG
CAAGAATCAAATGGTCAAATTGATGAAAGTCCAACAATGAGTAGAAACGGAACTCCCGAC
ATGGCACTAAGCAATCATAATCGACTCATCAGATCTGAAGCTATAAGAGCTCAGCAACAA
ATAATTGGTAAGCAAAAGTATGATTTGTCAAAATGGAAGTATTCAGAGCTTCGTGATGCT
ATCAACACAAGCTGTGATATTGAGTTACTTGAGGCATGTCGTCATGAATTTCATCGTCGT
CTTAAAGTGTATCATGCATGGAAAGCAAAGAATCGCAAACGCACTACAATGGATGAAAAT
GAGCGCGCTCCAAGAAGTGTAATGGAAAATGCCGGAAAAATTCCATTGCGTACTCAACAA
AAATCTTCTTCTGATCCTAATTCCGTTTCAATTCATCGCTACTTTCGCATTCCATTTATG
CGTCCTAACGGAAATACAAATGATAATACTAATCGAGGTTGGTGGTACGCACATTTTGAT
GGTTCGTATGTTGCACGGCAAATGGAATTACATGCAGAAAAACCTCCAATTTTATTGATT
GCCGGTGTGGATGATATGCAAATGTGTGAATTAAGTTTGGAAGAGACAGGACTAACTCGA
AAAAGAGGTGCAGAAATATTAGAACATGAATTTAATCGTGAATGGGAACGTCATGGAGGT
AAACCCTATAAGGTGCAAAATGGAAAGTCTTAA
>g3978.t4 Gene=g3978 Length=288
MELRRKQEEAERLRLEEEDRRAALLLQAQLEKEAQEDSKYRQQLEQERRDHELALRLAQE
SNGQIDESPTMSRNGTPDMALSNHNRLIRSEAIRAQQQIIGKQKYDLSKWKYSELRDAIN
TSCDIELLEACRHEFHRRLKVYHAWKAKNRKRTTMDENERAPRSVMENAGKIPLRTQQKS
SSDPNSVSIHRYFRIPFMRPNGNTNDNTNRGWWYAHFDGSYVARQMELHAEKPPILLIAG
VDDMQMCELSLEETGLTRKRGAEILEHEFNREWERHGGKPYKVQNGKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3978.t4 | Coils | Coil | Coil | 3 | 23 | - |
| 4 | g3978.t4 | Coils | Coil | Coil | 27 | 61 | - |
| 2 | g3978.t4 | PANTHER | PTHR13140:SF788 | MYOSIN VIB | 1 | 282 | 5.0E-76 |
| 3 | g3978.t4 | PANTHER | PTHR13140 | MYOSIN | 1 | 282 | 5.0E-76 |
| 1 | g3978.t4 | Pfam | PF16521 | Myosin VI cargo binding domain | 190 | 278 | 7.4E-45 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
