General information for g6004.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Symplekin.
Parent gene
- The parent gene g6004 is located on chr_2: 13459949..13463541 (- 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 | g6004 | g6004.t2 | TTS | g6004.t2 | 13459898 | 13459898 |
| chr_2 | g6004 | g6004.t2 | isoform | g6004.t2 | 13459949 | 13460998 |
| chr_2 | g6004 | g6004.t2 | exon | g6004.t2.exon1 | 13459949 | 13460502 |
| chr_2 | g6004 | g6004.t2 | cds | g6004.t2.CDS1 | 13459949 | 13460502 |
| chr_2 | g6004 | g6004.t2 | exon | g6004.t2.exon2 | 13460571 | 13460789 |
| chr_2 | g6004 | g6004.t2 | cds | g6004.t2.CDS2 | 13460571 | 13460772 |
| chr_2 | g6004 | g6004.t2 | exon | g6004.t2.exon3 | 13460851 | 13460998 |
| chr_2 | g6004 | g6004.t2 | TSS | g6004.t2 | NA | NA |
Sequences
>g6004.t2 Gene=g6004 Length=921
GATGTGAAAAGAGTTATTTTGAGAAGTATTGAAGTTCCTATTAAAAAATTGGGCACAGAT
TCGAAGGAAATTTTCAAAATTCTTGAAACATGTGCTAAAGGAACAGAAACTCTTGTAACG
AGAATCATTTACATTTTAACAGAAACACAAACACCTTCACTTGAAATGGTTGAAAAAGTT
AAAAATTTGTACAATACAAAACTCAATGATGTTCGCATTCTCATTCCAATAATTCTTCAC
ATACCGAAAAAGGAAATCATTGCAGCATTGCCAAAATTTTTAAAACTTAATCCACAACTT
ATGAAAGACGTTTTTCTTCGACTTTTGGGAGTTAAAAATGACGCATTAAAAAGCAACTTA
CAGCCAATTACACCGACAGAATTACTTGTTGCACTTCATGCAATTGATACATCTCAAGCT
GAATTAAGATTGATAGTGAAAGCAACATCATTGTGTTTGGCAGAGAAAGAAGTTTATACG
CATGAAGTACTTGGTGTTGTAATGCAACAGTTGGTTGAAATGAATCCTCTTCCTACATTA
TTAATGAGAACTGTAATTCAATCACATACAATGTATCCAAGACTTTCTGGATTTATTACA
AATCTTTTACAACGATTAATTGTGAAACAAGTGTGGAAAAATAAATTGATATGGGATGGA
TTTGTAAAATGCTGCCAGAGACTTCAATGTATGGGTGTTTTAGTTCAACTACCAACAGCA
CAATTGCAAGATGCATTAACAATTTGTCCAGATTTAAAAAATCCATTAATTGAATATGCA
CGTGAAATGAATAAACATCAAATGGGTCATGTAACACAAAACATTCTCGATATATTAGGC
GAAGGACAATCTTCAACAACGGGAGCAATTAAATCAGAACCTATGGATGTAGATGCTGAT
GCTGCACCACCTGGAATTTAA
>g6004.t2 Gene=g6004 Length=251
MVEKVKNLYNTKLNDVRILIPIILHIPKKEIIAALPKFLKLNPQLMKDVFLRLLGVKNDA
LKSNLQPITPTELLVALHAIDTSQAELRLIVKATSLCLAEKEVYTHEVLGVVMQQLVEMN
PLPTLLMRTVIQSHTMYPRLSGFITNLLQRLIVKQVWKNKLIWDGFVKCCQRLQCMGVLV
QLPTAQLQDALTICPDLKNPLIEYAREMNKHQMGHVTQNILDILGEGQSSTTGAIKSEPM
DVDADAAPPGI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6004.t2 | PANTHER | PTHR15245 | SYMPLEKIN-RELATED | 2 | 227 | 0 |
| 3 | g6004.t2 | PANTHER | PTHR15245:SF20 | SYMPLEKIN | 2 | 227 | 0 |
| 1 | g6004.t2 | Pfam | PF12295 | Symplekin tight junction protein C terminal | 15 | 192 | 0 |
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.
