General information for g5755.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative SET and MYND domain-containing protein 4.
Parent gene
- The parent gene g5755 is located on chr_2: 11681632..11684487 (- 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 | g5755 | g5755.t1 | isoform | g5755.t1 | 11679425 | 11681632 |
| chr_2 | g5755 | g5755.t1 | exon | g5755.t1.exon1 | 11679425 | 11679758 |
| chr_2 | g5755 | g5755.t1 | cds | g5755.t1.CDS1 | 11679425 | 11679758 |
| chr_2 | g5755 | g5755.t1 | exon | g5755.t1.exon2 | 11679816 | 11680446 |
| chr_2 | g5755 | g5755.t1 | cds | g5755.t1.CDS2 | 11679816 | 11680446 |
| chr_2 | g5755 | g5755.t1 | exon | g5755.t1.exon3 | 11681056 | 11681632 |
| chr_2 | g5755 | g5755.t1 | cds | g5755.t1.CDS3 | 11681056 | 11681632 |
| chr_2 | g5755 | g5755.t1 | TSS | g5755.t1 | NA | NA |
| chr_2 | g5755 | g5755.t1 | TTS | g5755.t1 | NA | NA |
Sequences
>g5755.t1 Gene=g5755 Length=1542
ATGGAAAAATCAAATGAAAAGTCAATAATTTTTAGGCAAGAAGGAAATGAATTTTATAAA
AAACGTGAATTCTTATCAGCACTTTTAAAATACAATCAAAGTTTGTGTTATGCTGAGAAA
AATAGTGAAAATCTTGCTCATGCATATGCAAATCGTTCCGCTGTGTATTTTGAAATGAAA
CTCTATGAAAAATGTCTTAGTAACATTAATTATGCAATTTCTAACAACTATCCTCAAGAA
AATTTAGAAATTTTAAACAAAAGAAGTGAAAAATGTAAAGATCAAGTGAATAAAATCTAT
GAAAATTACTTTAAATTATCACATCAAGCCAATAAAAGAATTCCCTTCATAGCCAGTAGT
TTACAATTAAATCATGACACAAAATATGGCAAACATGTTATTACTAATAAAAATCTCTCT
GTCGGCGACGTAATTGCAATTGAAAAACCGTTTTGTTGTGTTCCTATAATTGAATCACGC
TTTGTAAAAATTCCTGAATTGAATAATTACCAACGTTGCAATAATTGCTTGCGTGATAAT
CAATTAGATTTAACTCCGTGCAGTTTTTGCTGTCAAGTTATGTTTTGTTCAACAGACTGT
CAAAATCATGCAATGAGATTCTATCACAAATATGAATGTCCAATAATATCTGAATTACTA
AAATCAGGCAGCATAAACATGGCCTTAAGAATATTCTTTATAGGCTTATCAATATTTGAC
AATGATATCGAAAAATTTAAAAAATGTGTTAATGAAAATCGAAATGCTTCTAAAACAATC
TTTGATTATAATTTTTCATCAGTTGAAAATGAAGATTATTTGAAAAATTACTTTTTGTCG
CTTATTTGTCTCTCACGAAGCACAAAAAAATTTTCATTGACGCCATATGAAAATATTCTT
AGCACACATCCACTGTTGCAAGCAGTTTTTAATGAAAACCGTGAATTTATTCTCGATTTC
ATACAACGTCAATGTCAAATATCTGATCATAATTTTCATGGAATATTCAGTTCAAGTTTA
AGTGCAAGCGATACATTGAGTGACATGAGAAATCTTCAAATGTCAATTGGTTCTGGGTCT
TTACCTTTTGCTAGTCTTATAAATCACAGCTGTAGTCCAAATGTCATGAGAATTTGTGAG
GATGGAAAAGTTGTTTTCATAGTTTGTCGACCGATTCAAAAAGGATCACAAATATTTGAC
TGTTATAAGGATAATTTCTTGATGGAATCAAAAGAATCGCGACAATTGAAACTTTTCAAT
GAATTTGCATTCAAATGTGAATGTGAAGCTTGTGAGAAAAATTGGCCAACTTTTAAAGCT
CTAACAATGAAAGATGCAAAATTAATGAAAATTGCAAAGAAACTTAATGAAGAAATGCAA
ATAATCATCAATAATCGCAATCAAACATCCAAAAAAGTTCAAATCTGTAAAGAAATTTTG
CAGAAAAATTTTGAAAATTATCCATCGATGGAACTATGCATTATACAGAAAATTTTTGCA
GCTTTATGTTTAAAATTGGCTGAATGCAAAGTTCTTTTTTAA
>g5755.t1 Gene=g5755 Length=513
MEKSNEKSIIFRQEGNEFYKKREFLSALLKYNQSLCYAEKNSENLAHAYANRSAVYFEMK
LYEKCLSNINYAISNNYPQENLEILNKRSEKCKDQVNKIYENYFKLSHQANKRIPFIASS
LQLNHDTKYGKHVITNKNLSVGDVIAIEKPFCCVPIIESRFVKIPELNNYQRCNNCLRDN
QLDLTPCSFCCQVMFCSTDCQNHAMRFYHKYECPIISELLKSGSINMALRIFFIGLSIFD
NDIEKFKKCVNENRNASKTIFDYNFSSVENEDYLKNYFLSLICLSRSTKKFSLTPYENIL
STHPLLQAVFNENREFILDFIQRQCQISDHNFHGIFSSSLSASDTLSDMRNLQMSIGSGS
LPFASLINHSCSPNVMRICEDGKVVFIVCRPIQKGSQIFDCYKDNFLMESKESRQLKLFN
EFAFKCECEACEKNWPTFKALTMKDAKLMKIAKKLNEEMQIIINNRNQTSKKVQICKEIL
QKNFENYPSMELCIIQKIFAALCLKLAECKVLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5755.t1 | Coils | Coil | Coil | 452 | 472 | - |
| 8 | g5755.t1 | Gene3D | G3DSA:1.25.40.10 | - | 1 | 117 | 1.1E-9 |
| 3 | g5755.t1 | PANTHER | PTHR47111 | BCDNA.LD29892 | 2 | 506 | 3.2E-101 |
| 1 | g5755.t1 | Pfam | PF01753 | MYND finger | 173 | 213 | 5.1E-5 |
| 2 | g5755.t1 | Pfam | PF00856 | SET domain | 335 | 402 | 3.1E-12 |
| 7 | g5755.t1 | ProSitePatterns | PS01360 | Zinc finger MYND-type signature. | 173 | 213 | - |
| 11 | g5755.t1 | ProSiteProfiles | PS50280 | SET domain profile. | 119 | 403 | 9.159 |
| 10 | g5755.t1 | ProSiteProfiles | PS50865 | Zinc finger MYND-type profile. | 173 | 213 | 9.14 |
| 4 | g5755.t1 | SUPERFAMILY | SSF48452 | TPR-like | 9 | 77 | 2.05E-9 |
| 5 | g5755.t1 | SUPERFAMILY | SSF82199 | SET domain | 118 | 429 | 1.57E-19 |
| 6 | g5755.t1 | SUPERFAMILY | SSF144232 | HIT/MYND zinc finger-like | 169 | 218 | 8.02E-9 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5755/g5755.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5755.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K24634 (SET and MYND domain-containing protein 4 [EC:2.1.1.-])
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.
