Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttgtacacactcttcaaattttgaatttgccaagggtttggagaccatgtgcttcacattcctctgtggaattctatttcgcagtctctacagttttttgttgcttttcgaggactgttgtaacaattcaacacttctgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAAAAATCTGGTGCACAACGAGCAGCAGCTGCTCACGGCCTCGCGCTAGTTG

Basic information

species Physcomitrella patens
transcript PP1S61_17V6.2
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208364085|gb|DC943397.1|DC943397
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|18343395|gb|BJ175433.1|BJ175433
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|67719202|gb|BJ969461.1|BJ969461
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|162192829|gb|FC370161.1|FC370161
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|208350927|gb|DC910474.1|DC910474
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|100394127|gb|BY971952.1|BY971952
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAANACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|100421061|gb|BY993592.1|BY993592
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|100383603|gb|BY950387.1|BY950387
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAANACTTCATCCCA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|208345645|gb|DC905603.1|DC905603
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|162267025|gb|FC443074.1|FC443074
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|208384596|gb|DC907083.1|DC907083
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
EST: gi|208344728|gb|DC905177.1|DC905177
EST:     TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCG                         GTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA
genomic: TGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 15 (upstream exon), 33 (downstream exon)
Score: 7

TGGTTTCAATCGCCGTTACAAGCATGAAAGTAGCTCCGTCGGATGTCCTATGACGTTCACCATCTTCTTCCCACCTGCGGCAGATTCGAGCAAAGTACCGgtgggttgta ... tgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAAAAATCTGGTGCACAACGAGCAGCAGCTGCTCACGGCCTCGCGCTAGTTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttgttgcttttcgaggactgttgtaacaattcaacacttctgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAAAAATCTGGTGCACAACGAGCAGCAGCTGCTCACGGCCTCGCGCTAGTTG
                         ttgtaac  putative branch site (score: 7)
                                       cacttct  putative PPT
                            taacaatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggttgtacacactcttcaaattttgaatttgccaagggtttggagaccatgtgcttcacattcctctgtggaattctatttcgcagtctctacagttttttgttgcttttcgaggactgttgtaacaattcaacacttctgtgtgacagGTTTTGTACTGGCTATCAGGGTTGACGTGCAACGACGAAAACTTCATCCAAAAATCTGGTGCACAACGAGCAGCAGCTGCTCACGGCCTCGCGCTAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT