General information for g6409.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6409 is located on chr_2: 16881171..16882331 (- 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 | g6409 | g6409.t4 | isoform | g6409.t4 | 16881171 | 16882331 |
| chr_2 | g6409 | g6409.t4 | exon | g6409.t4.exon1 | 16881171 | 16882254 |
| chr_2 | g6409 | g6409.t4 | cds | g6409.t4.CDS1 | 16881173 | 16881658 |
| chr_2 | g6409 | g6409.t4 | exon | g6409.t4.exon2 | 16882309 | 16882331 |
| chr_2 | g6409 | g6409.t4 | TSS | g6409.t4 | 16882430 | 16882430 |
| chr_2 | g6409 | g6409.t4 | TTS | g6409.t4 | NA | NA |
Sequences
>g6409.t4 Gene=g6409 Length=1107
ATGGAAGTTACAAAGCAAAGTAAATTTTAAAGATTGTCTCGTTGAAATTACAAAAGATAT
TGAAGAAGCTCATTTTATTAGTATTGATACTGAATTTACCGGATTGACAAGCGAGCGAAA
TATTTTGCCATTTGACACGAGTGAAGAATACTATGAAAAACTTTTCCGATCAACAAAAGG
TTTTATTATAGTGCAATTAGGGATCTCATTATTTAAAAAAGATCCAGGTGGAGAAAAAGT
GAAAGTAAAATCTTACAATATTTACACTTACCCGCAATCGAGTCTTGCTACTTTTCTTTG
TCAAAGCCAATCATTTTCATTTTTAGCCGAAAATGGTTTTGATTTCAATAAATTGTTCTC
TAGTGGTGTCGGCGTTTGTAATGAAAAACAAGAAGAAAAGTTAAGACAAGAAGTTAAAGA
ACGTCAAGAATTTAGACAAGAACAGATAAAAATACGTACAAGTGATGAACAAGTTGATAC
AAGTAGCAGAAATTTTTTACCTGTACCTGAAAATGAAAAAGAGTTAATTGACAATGCAAA
GGAGAAGATTCAACAAGTGATTGATAATAAAATTCTTGAGGCAAAATTTGAGAAACTCAA
TGGTTTCCAAAGGAAATTGATGTATGAACTAATTGAAAGAGATTTTAACAATAAAGTCTC
TACATTGACTAAAAATGGAGATAATTATCAAAAAATGATGGTAGTTACTTCTAAAAGAAC
TCTTGAAGATGAATTAAAATTGGAAAAGGACAAAATTCGGGACGATGAAAATTCTTTGAT
TGAAAAAATTGGTATTCGTTTATTAATGAAAGAAATTTCTAAGTCAAAAAAGCCTATTGT
GGCTCATAACTGTTTATTAGACTTCTTCTACATCTTAACGCAATGTTTTGAAGATTTACC
AGAAAATTATAATGATTTCAAGAAACTTATTCATCGCATATTCCCAAACATTATTGATAC
AAAGTTTATTGCACACTCTGACCACTTGAAAGAATTCTTCTCATCGACTGTATTAAATCA
AGTTCTTGAACGTCTACAGAAACCTCCATTCAAGGAAATTGAATTAGAATGGGAAAATCC
TTATAATACATATAGTTTAAAATCACC
>g6409.t4 Gene=g6409 Length=162
MYELIERDFNNKVSTLTKNGDNYQKMMVVTSKRTLEDELKLEKDKIRDDENSLIEKIGIR
LLMKEISKSKKPIVAHNCLLDFFYILTQCFEDLPENYNDFKKLIHRIFPNIIDTKFIAHS
DHLKEFFSSTVLNQVLERLQKPPFKEIELEWENPYNTYSLKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6409.t4 | Coils | Coil | Coil | 32 | 52 | - |
| 5 | g6409.t4 | Gene3D | G3DSA:3.30.420.10 | - | 6 | 162 | 9.1E-34 |
| 2 | g6409.t4 | PANTHER | PTHR15092 | POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1 | 2 | 159 | 8.1E-26 |
| 3 | g6409.t4 | PANTHER | PTHR15092:SF44 | POLY(A)-SPECIFIC RIBONUCLEASE PARN | 2 | 159 | 8.1E-26 |
| 1 | g6409.t4 | Pfam | PF04857 | CAF1 family ribonuclease | 25 | 147 | 4.4E-29 |
| 4 | g6409.t4 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 55 | 139 | 1.44E-18 |
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:0003676 | nucleic acid binding | MF |
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. There were no conditions that were differentially expressed