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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcttcatcagttcgtattgtactagttttctagatgcttcacttgccaatgatttctaattggatcctggtacatgtgcaattggttgaaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG

Basic information

species Physcomitrella patens
transcript PP1S14_318V6.2
intron # 8
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|162159572|gb|FC335750.1|FC335750
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|18336897|gb|BJ168920.1|BJ168920
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTC
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCT-CCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTC
EST: gi|67727809|gb|BJ978068.1|BJ978068
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162184795|gb|FC361097.1|FC361097
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67728278|gb|BJ978537.1|BJ978537
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67726888|gb|BJ977147.1|BJ977147
EST:     TGAACCAGGTTCTGGGTGATCGGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67728007|gb|BJ978266.1|BJ978266
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|7582787|gb|AW698951.1|AW698951
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|37836566|gb|BJ594574.1|BJ594574
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67721922|gb|BJ972181.1|BJ972181
EST:     GATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: GATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67725789|gb|BJ976048.1|BJ976048
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67723947|gb|BJ974206.1|BJ974206
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|37846703|gb|BJ604711.1|BJ604711
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|208373205|gb|DC944904.1|DC944904
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162235943|gb|FC411686.1|FC411686
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|18340442|gb|BJ172470.1|BJ172470
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162245025|gb|FC424983.1|FC424983
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162195398|gb|FC370867.1|FC370867
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67692593|gb|BJ952826.1|BJ952826
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|67724183|gb|BJ974442.1|BJ974442
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|37849081|gb|BJ607089.1|BJ607089
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|37823060|gb|BJ581126.1|BJ581126
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162245026|gb|FC424984.1|FC424984
EST:     TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT
EST: gi|162270584|gb|FC446509.1|FC446509
EST:     TGAACCAGGTTTTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCG                         CTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTTT
genomic: TGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTCTGTGCTTTCATCGgtaagaacct ... aaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccaatgatttctaattggatcctggtacatgtgcaattggttgaaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG
          ttctaat  putative branch site (score: 2)
        atttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcttcatcagttcgtattgtactagttttctagatgcttcacttgccaatgatttctaattggatcctggtacatgtgcaattggttgaaaatgacagCTCCCTGGAGTAGATCCAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - tgcttca