General information for g6004.t1
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.t1 | TTS | g6004.t1 | 13459898 | 13459898 |
| chr_2 | g6004 | g6004.t1 | isoform | g6004.t1 | 13459949 | 13463541 |
| chr_2 | g6004 | g6004.t1 | exon | g6004.t1.exon1 | 13459949 | 13460502 |
| chr_2 | g6004 | g6004.t1 | cds | g6004.t1.CDS1 | 13459949 | 13460502 |
| chr_2 | g6004 | g6004.t1 | exon | g6004.t1.exon2 | 13460571 | 13460789 |
| chr_2 | g6004 | g6004.t1 | cds | g6004.t1.CDS2 | 13460571 | 13460789 |
| chr_2 | g6004 | g6004.t1 | exon | g6004.t1.exon3 | 13460851 | 13463138 |
| chr_2 | g6004 | g6004.t1 | cds | g6004.t1.CDS3 | 13460851 | 13463138 |
| chr_2 | g6004 | g6004.t1 | exon | g6004.t1.exon4 | 13463198 | 13463400 |
| chr_2 | g6004 | g6004.t1 | cds | g6004.t1.CDS4 | 13463198 | 13463400 |
| chr_2 | g6004 | g6004.t1 | exon | g6004.t1.exon5 | 13463458 | 13463541 |
| chr_2 | g6004 | g6004.t1 | cds | g6004.t1.CDS5 | 13463458 | 13463541 |
| chr_2 | g6004 | g6004.t1 | TSS | g6004.t1 | 13463621 | 13463621 |
Sequences
>g6004.t1 Gene=g6004 Length=3348
ATGGCTTCAATAATTCCAGGCTTGTTGATAGATGAGTCTGAGACTCCATTTAGTCAGGAA
GATGTAGTTCGAGCTCGTACATCTATTATGGAAAATCTCAATCAACTCTTGACTGCCTCA
TCACCATCAACTAAAATTGAGCTTGTGACAAAGATTCAGGAGCAAGTCTTAAAATGGGCA
CCTGCAATGCGTGTCCTCGAAGAAGTCATTGATGATGTACTTGCACTTAGTCTTGATCAG
AATCAAGATGTAAAGAAATCAATAATTAATTTTATTGAAGAAGTCTGTAAACAAAGAATT
AGAATGCTTCCGAAAGTTATAAAATGCTTAACAATGCTTTTAAGAGAAGAATCTGCTATG
GTCATAAAACGAGTTATGCAAGCTTGTGGAACAATTTACAAAGCAACGCTACAATGGATG
TGCACATCAGAGGATGTAACTGAAGAAATGAATGAATGTTGGGATCAATTATGCTTCATA
AAATTGCAAATTTTAGATATGATTGATCATGAAAACGATGGAATAAGAACCAATGCAATC
AAATTTCTCGAAATTGTTGTACTTTTGCAAACTCACTCCGACGATGATAGTATGAAACGT
GAAAATGATTTCTCACTTGATGATGTGCCATTAACTCTTGCACATATTCGAAGACGAAAA
CTCGAAGAAGAAGCAGTTAATATTTTTGATCTTCTACTAAAATTCCATGGCGCTTCTCAC
ATTTCTTCTGTTAATTTGATCGCATGTACTGGAACATTATGTACGATTGCAAAAATGAGA
CCAAAACTTATGGGTCAAGTAGTTGAAGCGCTCAAATTACTTCATTCAAATCTACCACCA
ACACTCACAAATTCTCAAGTTGCATCGGTTCGAAAAAATCTCAAAATGCAATTTGTAAAT
TTGCTCAAGCAGCCAGCAAGTTATGAATGGAGATCTATGATTGTACCAATTTTGTCAGAT
TTAGGTGCAAGTCAAAATGAAATAAACAGAGCAATTCCAAAGATGAGTCAGAGTGAGTTG
TTAAAGAGAAAACAAAAGGCTCAAGAAAATGAAGATATTAGAAAGGCAAAAGTTGCAAGA
TTAGAATTAGAAGAGAAAGAGCGAACAGCTCAAGAACTTGCAATTTTAAAAGAGATGGAA
GATGATGAACTTATTTTAGAACAAGAAAGAAAATGTGAATTAATAAATGAAAAATTTATT
GCGGATGCTATAAAATCTATAGATGTAGCTTCACAATTAGTCATTAATTCTATGATAAAT
TTACCTGATAAAATTCCAGCAGAATTTATTAAAAATTATCAACCAGCAACTACAGTTTTA
TCAATTCAAGATCAAATTAATATCATTGCTAAAACATTTGCATCTCAACTAACAGAATTG
AAACTTGGTCCTGGTGCCAAAGAACTTTTAGAAGTTAAGCCTTTAAAATCGAAAACTTCT
TTAAAAGAAGACAAAATATCAAAAGAGGACGATGATGAAGAATATCAAAAAGATGAAACC
ACACGAAAACTACGTGAAACACTTGCAAGAGTAAAACATCAACCAAAAATGAAACAGAGA
ATAAAGACATTAAAATTACATGAAATAACTAAACCACTTCCGAAAGAGTTAAAGCATCAG
TTCCTTAATGATGCAGTGAGAAAAATCCTAAATTGTGAACGACAAGCTGTTATTGGTGGA
GCTGGTTTCAAACGTAAAAAAATCATTACAGTGTTTGCATCAACGTTTATGCCTAGCGTT
CGCGAAATAATAATGGAATATATCATGGAAAATATTGTTAAAAGATTTGATTTGGCTTTC
ATGTGGTTATTTGAAGAATATAGCTTAATGCAAGGTTTCACAAGATTTTCATATGTAAAA
TCAGAACACAAACATGACTATGCTTATAACAGACTTCTCGCCGAGTTCATTTTGAAAATT
TTCAATCGTGGAACTGAATTTCGTGAAAGAGAAAGCTTACTGAAAAGACTTTATCTTGAA
GCACCTTTGATTAGTGACGAAAGTATAGATATATTAACCAGAATTTCTGAGCATGATGAT
CTTTATGAATGTGGATTAGTTTTATTAAAAGATTTGTTAATTCGACGACCACCAAAGGAG
GAACAATTATTAATGACACTTTTGAAATTTGCAGTACATCAAAAAACATCGATTCGTGAG
AAGGCGATTGAAAATGTTATGATCGTTTATAATATGCATCAAATTCTTGTTGAAAATATT
GAAATATTTGCCATAAAATTGGTCAAAATGTTAGAAAAACCCACACCAACTTCTGATGTG
CTTAATATTCTATCAATGCAAAATGAAAATGTTGAAGCTTGGACTGAAGATATGATTAAA
TCATGTCTTAATCTCTATCTTACAATTTTGCCCTATAACGAAATGCTATTACCTGGTTTA
GTGCCTGTTTATGTTGAATCAACTTCAGATGTGAAAAGAGTTATTTTGAGAAGTATTGAA
GTTCCTATTAAAAAATTGGGCACAGATTCGAAGGAAATTTTCAAAATTCTTGAAACATGT
GCTAAAGGAACAGAAACTCTTGTAACGAGAATCATTTACATTTTAACAGAAACACAAACA
CCTTCACTTGAAATGGTTGAAAAAGTTAAAAATTTGTACAATACAAAACTCAATGATGTT
CGCATTCTCATTCCAATAATTCTTCACATACCGAAAAAGGAAATCATTGCAGCATTGCCA
AAATTTTTAAAACTTAATCCACAACTTATGAAAGACGTTTTTCTTCGACTTTTGGGAGTT
AAAAATGACGCATTAAAAAGCAACTTACAGCCAATTACACCGACAGAATTACTTGTTGCA
CTTCATGCAATTGATACATCTCAAGCTGAATTAAGATTGATAGTGAAAGCAACATCATTG
TGTTTGGCAGAGAAAGAAGTTTATACGCATGAAGTACTTGGTGTTGTAATGCAACAGTTG
GTTGAAATGAATCCTCTTCCTACATTATTAATGAGAACTGTAATTCAATCACATACAATG
TATCCAAGACTTTCTGGATTTATTACAAATCTTTTACAACGATTAATTGTGAAACAAGTG
TGGAAAAATAAATTGATATGGGATGGATTTGTAAAATGCTGCCAGAGACTTCAATGTATG
GGTGTTTTAGTTCAACTACCAACAGCACAATTGCAAGATGCATTAACAATTTGTCCAGAT
TTAAAAAATCCATTAATTGAATATGCACGTGAAATGAATAAACATCAAATGGGTCATGTA
ACACAAAACATTCTCGATATATTAGGCGAAGGACAATCTTCAACAACGGGAGCAATTAAA
TCAGAACCTATGGATGTAGATGCTGATGCTGCACCACCTGGAATTTAA
>g6004.t1 Gene=g6004 Length=1115
MASIIPGLLIDESETPFSQEDVVRARTSIMENLNQLLTASSPSTKIELVTKIQEQVLKWA
PAMRVLEEVIDDVLALSLDQNQDVKKSIINFIEEVCKQRIRMLPKVIKCLTMLLREESAM
VIKRVMQACGTIYKATLQWMCTSEDVTEEMNECWDQLCFIKLQILDMIDHENDGIRTNAI
KFLEIVVLLQTHSDDDSMKRENDFSLDDVPLTLAHIRRRKLEEEAVNIFDLLLKFHGASH
ISSVNLIACTGTLCTIAKMRPKLMGQVVEALKLLHSNLPPTLTNSQVASVRKNLKMQFVN
LLKQPASYEWRSMIVPILSDLGASQNEINRAIPKMSQSELLKRKQKAQENEDIRKAKVAR
LELEEKERTAQELAILKEMEDDELILEQERKCELINEKFIADAIKSIDVASQLVINSMIN
LPDKIPAEFIKNYQPATTVLSIQDQINIIAKTFASQLTELKLGPGAKELLEVKPLKSKTS
LKEDKISKEDDDEEYQKDETTRKLRETLARVKHQPKMKQRIKTLKLHEITKPLPKELKHQ
FLNDAVRKILNCERQAVIGGAGFKRKKIITVFASTFMPSVREIIMEYIMENIVKRFDLAF
MWLFEEYSLMQGFTRFSYVKSEHKHDYAYNRLLAEFILKIFNRGTEFRERESLLKRLYLE
APLISDESIDILTRISEHDDLYECGLVLLKDLLIRRPPKEEQLLMTLLKFAVHQKTSIRE
KAIENVMIVYNMHQILVENIEIFAIKLVKMLEKPTPTSDVLNILSMQNENVEAWTEDMIK
SCLNLYLTILPYNEMLLPGLVPVYVESTSDVKRVILRSIEVPIKKLGTDSKEIFKILETC
AKGTETLVTRIIYILTETQTPSLEMVEKVKNLYNTKLNDVRILIPIILHIPKKEIIAALP
KFLKLNPQLMKDVFLRLLGVKNDALKSNLQPITPTELLVALHAIDTSQAELRLIVKATSL
CLAEKEVYTHEVLGVVMQQLVEMNPLPTLLMRTVIQSHTMYPRLSGFITNLLQRLIVKQV
WKNKLIWDGFVKCCQRLQCMGVLVQLPTAQLQDALTICPDLKNPLIEYAREMNKHQMGHV
TQNILDILGEGQSSTTGAIKSEPMDVDADAAPPGI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6004.t1 | Coils | Coil | Coil | 344 | 383 | - |
| 6 | g6004.t1 | Gene3D | G3DSA:1.25.10.10 | - | 14 | 353 | 2.5E-114 |
| 3 | g6004.t1 | PANTHER | PTHR15245 | SYMPLEKIN-RELATED | 31 | 1091 | 1.4E-238 |
| 4 | g6004.t1 | PANTHER | PTHR15245:SF20 | SYMPLEKIN | 31 | 1091 | 1.4E-238 |
| 1 | g6004.t1 | Pfam | PF11935 | Domain of unknown function (DUF3453) | 120 | 335 | 5.9E-54 |
| 2 | g6004.t1 | Pfam | PF12295 | Symplekin tight junction protein C terminal | 879 | 1056 | 1.6E-58 |
| 5 | g6004.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 26 | 1050 | 5.38E-9 |
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 transcript has been annotated with K06100 (symplekin)
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.
