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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatattttccgtggcttgtgtaccagcgttcctccctcagtcgatgtttctaaaatgatcaactggtttgtttactacctcagatttttgaaattgatgttttcctttttgcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTGGTTGAACCGAAATCCAGATGAATCTTCTGGCGGTGAGTTGGTTTTAGGT

Basic information

species Physcomitrella patens
transcript PP1S93_73V6.2
intron # 4
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|208356135|gb|DC902213.1|DC902213
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACANCATGTTGGATCANGGGCTTGTGAAGGANCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100359537|gb|BY947032.1|BY947032
EST:     CTTGGTCTTGGATTTNAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100409102|gb|BY991858.1|BY991858
EST:     TTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCAATG                         GTACA-CATGTTGGATCAGGGGCTTGTGAA
genomic: TTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCA-TGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAA
EST: gi|162157639|gb|FC332961.1|FC332961
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162153928|gb|FC329435.1|FC329435
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGNGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162231957|gb|FC409031.1|FC409031
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162180470|gb|FC356112.1|FC356112
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|208391424|gb|DC937572.1|DC937572
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACANCATGTTGGATCAGGGGCTTGTGAAGGANCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100367922|gb|BY948157.1|BY948157
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGGATCAGGG-CTTGTGAAGNAGCCTGTTTTCTC
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGG-ATCAGGGGCTTGTGAAGGAGCCTGTTTTCTC
EST: gi|67718260|gb|BJ968519.1|BJ968519
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162274216|gb|FC449976.1|FC449976
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCANGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162188198|gb|FC363964.1|FC363964
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|208361291|gb|DC930330.1|DC930330
EST:     CTTGNTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCANGGGCTTGTGAA
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAA
EST: gi|162182309|gb|FC357180.1|FC357180
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCANGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100388408|gb|BY952010.1|BY952010
EST:     TGGTCTTGGATTTAAGGAGATTTCTGTNAAACAGG-TGACTCCTCCCATG                         GTACA-CATGGTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTTC
genomic: TGGTCTTGGATTTAAGGAGATTTCTGT-AAACAGGGTGACTCCTCC-ATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTT-C
EST: gi|162266083|gb|FC442768.1|FC442768
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGAT
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGAT
EST: gi|162277812|gb|FC454275.1|FC454275
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100387632|gb|BY951632.1|BY951632
EST:     TTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCCTC-ATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGAAGC-TGTTTTCTCTTTCT
genomic: TTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCC-TCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCT
EST: gi|67508427|gb|BJ941294.1|BJ941294
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATC
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATC
EST: gi|100446181|gb|CJ970480.1|CJ970480
EST:     CTTGGTCTTGGATTTAAGGAGATT-CTGTAA-CAGGGTGACTCCTCN-TG                         GTACANCATGTTGGATCAGGGGCTTGTGAA
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAA
EST: gi|162255640|gb|FC431638.1|FC431638
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162174833|gb|FC351625.1|FC351625
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATC
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATC
EST: gi|162262898|gb|FC439291.1|FC439291
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162192060|gb|FC367273.1|FC367273
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|162192780|gb|FC370138.1|FC370138
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
EST: gi|100410404|gb|BY992089.1|BY992089
EST:     CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCAATG                         GTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG
genomic: CTTGGTCTTGGATTTAAGGAGATTTCTGTAAACAGGGTGACTCCTCCATGgtaagtatat ... gcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtttactacctcagatttttgaaattgatgttttcctttttgcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTGGTTGAACCGAAATCCAGATGAATCTTCTGGCGGTGAGTTGGTTTTAGGT
                          aattgat  putative branch site (score: 4)
                                tgttttcctttttgct  CT-rich tract
                  atttttgaaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatattttccgtggcttgtgtaccagcgttcctccctcagtcgatgtttctaaaatgatcaactggtttgtttactacctcagatttttgaaattgatgttttcctttttgcttcttcagGTACAACATGTTGGATCAGGGGCTTGTGAAGGAGCCTGTTTTCTCTTTCTGGTTGAACCGAAATCCAGATGAATCTTCTGGCGGTGAGTTGGTTTTAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG