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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcatttctgtcgagaaaatcgtatgtttgtatattcgtaaaagtagagtatctgttctgtgaactttgaccatagcgtcacgtcgcgattaaagatagttcctgttatctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAGCACGAAGTTAACGTCG

Basic information

species Physcomitrella patens
transcript PP1S52_45V6.1
intron # 6
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|208385483|gb|DC956667.1|DC956667
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|67727266|gb|BJ977525.1|BJ977525
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208363380|gb|DC946978.1|DC946978
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGGCGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|67724954|gb|BJ975213.1|BJ975213
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208386909|gb|DC956906.1|DC956906
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|67721269|gb|BJ971528.1|BJ971528
EST:     TGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: TGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208386836|gb|DC953503.1|DC953503
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|162183531|gb|FC359629.1|FC359629
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|162226789|gb|FC403822.1|FC403822
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|162254133|gb|FC429657.1|FC429657
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTTGGGGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208399439|gb|DC924869.1|DC924869
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208394499|gb|DC953538.1|DC953538
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208387574|gb|DC953316.1|DC953316
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|37851675|gb|BJ609683.1|BJ609683
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|208366252|gb|DC943812.1|DC943812
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|18337911|gb|BJ169935.1|BJ169935
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|162166325|gb|FC342918.1|FC342918
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|67725320|gb|BJ975579.1|BJ975579
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
EST: gi|37850094|gb|BJ608102.1|BJ608102
EST:     CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTT                         AACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG
genomic: CAATTAAAGCTATCCAAACTGGATGGCTGCACCCATCAATTAACCAATTTgtaagtgcat ... tctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgaccatagcgtcacgtcgcgattaaagatagttcctgttatctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAGCACGAAGTTAACGTCG
 ctttgac  putative branch site (score: 4)
                         attaaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcatttctgtcgagaaaatcgtatgtttgtatattcgtaaaagtagagtatctgttctgtgaactttgaccatagcgtcacgtcgcgattaaagatagttcctgttatctgttgcagAACCCAGAGGAGTCGGTGACGTTCGATACTGTGCCAAATGTGAAGAAGCAGCACGAAGTTAACGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC