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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggtgttaaatgagagatgttttttttcatgttcatgttacgtggaccgtgaatgctaggtatgttgctctgacacccccggtgaaaatgatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGA

Basic information

species Physcomitrella patens
transcript PP1S249_49V6.1
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|162238575|gb|FC418964.1|FC418964
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|18365712|gb|BJ197789.1|BJ197789
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162269518|gb|FC445074.1|FC445074
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|37826926|gb|BJ584938.1|BJ584938
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162263756|gb|FC438921.1|FC438921
EST:     TCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: TCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|22491699|gb|BU051622.1|BU051622
EST:     GCGGAGGCAACCTTGTTTGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: GCGGAGGCAACCATG-GCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162265957|gb|FC442960.1|FC442960
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|208372756|gb|DC952643.1|DC952643
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162201747|gb|FC377499.1|FC377499
EST:     CAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: CAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|18353808|gb|BJ185863.1|BJ185863
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|18325320|gb|BJ157316.1|BJ157316
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162243663|gb|FC420679.1|FC420679
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|37835281|gb|BJ593293.1|BJ593293
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162260417|gb|FC435043.1|FC435043
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|37845489|gb|BJ603497.1|BJ603497
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|67570411|gb|BJ943235.1|BJ943235
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|67693686|gb|BJ953919.1|BJ953919
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162226589|gb|FC402491.1|FC402491
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162244437|gb|FC422610.1|FC422610
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162260403|gb|FC435042.1|FC435042
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|67570144|gb|BJ942968.1|BJ942968
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162237156|gb|FC413523.1|FC413523
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162238574|gb|FC418963.1|FC418963
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|208375486|gb|DC937001.1|DC937001
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGACAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|7583876|gb|AW699778.1|AW699778
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|208392197|gb|DC957276.1|DC957276
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGACAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162237157|gb|FC413524.1|FC413524
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162244436|gb|FC422609.1|FC422609
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|18347837|gb|BJ179884.1|BJ179884
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|162263757|gb|FC438922.1|FC438922
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
EST: gi|37823882|gb|BJ581948.1|BJ581948
EST:     AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGG                         AGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA
genomic: AGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 62

TTAAGCGTGATTTTTCTTGGTGGAGATTTCTCTGCAGCGTAGGTGTCGTAAGCGGAGGCAACCATGGCGAAAAACTCGTTCAAGCAAGAGCATCCAATGGgtacgagcgt ... gatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccgtgaatgctaggtatgttgctctgacacccccggtgaaaatgatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGA
                       ctctgac  putative branch site (score: 62)
                                        aaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggtgttaaatgagagatgttttttttcatgttcatgttacgtggaccgtgaatgctaggtatgttgctctgacacccccggtgaaaatgatgaaacagAGAAGAGGCAAGCTGAGGCAGCAAGGATCCGTGACAAGTATCCTGACAGAATTCCTGTAATTGTGGAGAAAGCCGAAAAGAGTGACATCTCAGACATAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA