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

...atcctcaatgcgttctcaaaagatactcacgggaaaagaaatagtggttcctttgaattgcgtatgctgaattagcttttgttttatttggcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG

Basic information

species Physcomitrella patens
transcript PP1S91_247V6.1
intron # 3
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|208349685|gb|DC917863.1|DC917863
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|37852656|gb|BJ610664.1|BJ610664
EST:     NGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTNCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTT-CCC
EST: gi|208357611|gb|DC934091.1|DC934091
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAA                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTAC-ATCCT
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCT
EST: gi|100392213|gb|BY953250.1|BY953250
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|37821977|gb|BJ580043.1|BJ580043
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162181210|gb|FC357629.1|FC357629
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162214047|gb|FC389885.1|FC389885
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162178434|gb|FC354158.1|FC354158
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162181211|gb|FC357630.1|FC357630
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162151333|gb|FC327462.1|FC327462
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|100402373|gb|BY954803.1|BY954803
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|67694051|gb|BJ954284.1|BJ954284
EST:     ACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: ACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|100396841|gb|BY953854.1|BY953854
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|37850258|gb|BJ608266.1|BJ608266
EST:     GTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: GTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTT-CCC
EST: gi|208368318|gb|DC935673.1|DC935673
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTNGGANGTCATGCAGGCATTACNATCCTTCCCN
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162232671|gb|FC409222.1|FC409222
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|67693648|gb|BJ953881.1|BJ953881
EST:     ACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: ACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|208370637|gb|DC948230.1|DC948230
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162232670|gb|FC409221.1|FC409221
EST:     GCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: GCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|19784263|gb|BQ040147.1|BQ040147
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|100445737|gb|CJ970036.1|CJ970036
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGANGTCATGCAGGCATTACNATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|37840408|gb|BJ598416.1|BJ598416
EST:     TACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162214048|gb|FC389886.1|FC389886
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|208392060|gb|DC941908.1|DC941908
EST:     TGTACGAGCAAGAACTTTCCTAGCCCACAGGAAGGGTCT-AATGTGANAN                         ATGTCNATGTACNTGTNGTTGGAGGTCATGCAGGCAT
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCAT
EST: gi|67726305|gb|BJ976564.1|BJ976564
EST:     GGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: GGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162209149|gb|FC385368.1|FC385368
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
EST: gi|162151332|gb|FC327461.1|FC327461
EST:     TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAG                         ATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC
genomic: TGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCC

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: 35 (upstream exon), 27 (downstream exon)
Score: 14

AAGGGTACCTATGATCCCAAGAGGCTGTTTGGTGTCACCACCTTGGATGTTGTACGAGCAAGGACTTTCCTAGCCCACAGGAAGGGTCTTAATGTGAGAGgtgtgtatct ... gcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttcctttgaattgcgtatgctgaattagcttttgttttatttggcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG
                                              cctttgc  CT-rich tract
                               ttttgttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctcaatgcgttctcaaaagatactcacgggaaaagaaatagtggttcctttgaattgcgtatgctgaattagcttttgttttatttggcctttgcagATGTCGATGTACCTGTTGTTGGAGGTCATGCAGGCATTACCATCCTTCCCCTGTTTTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa