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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttttgataacttgttctcacacaggatttgtagacgaatttcattttttgaattctgtaaacgatctagtggggattgggcctccctatgtatgttgccattctgatgataatgtgtattggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCCACTTGTGGTGTAAAGAGCCTGTTGGATGAGGAAGCCGTTATGGTTGGAG

Basic information

species Physcomitrella patens
transcript PP1S3_353V6.2
intron # 5
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|19790424|gb|BQ041863.1|BQ041863
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|162160440|gb|FC337441.1|FC337441
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|100388487|gb|BY952089.1|BY952089
EST:     TCCGGCAGATTATCGCCACATGGAGGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGT-CCACTGGAAGCCC
genomic: TCCGGCAGATTATCGCCACATGGAGGG-TTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|162212518|gb|FC388494.1|FC388494
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|162269381|gb|FC445249.1|FC445249
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTC
EST: gi|162171823|gb|FC348973.1|FC348973
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|100355998|gb|BY946143.1|BY946143
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCCTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|100403993|gb|BY955201.1|BY955201
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCA-GGCTGGCAAAGAAACTTATGTAAAGTTCCACTGG
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGG
EST: gi|162190690|gb|FC367576.1|FC367576
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCA-GGCTGGCAAAGAAACTTATGTAAAGTTCCACTGG
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGG
EST: gi|162196447|gb|FC373047.1|FC373047
EST:     GGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: GGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|100385323|gb|BY950915.1|BY950915
EST:     TTCCGGCAGAATATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TGGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCAC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCAC
EST: gi|162277340|gb|FC453146.1|FC453146
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|100400264|gb|BY954390.1|BY954390
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACAAAGGCTGGCAAAGAA
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAA
EST: gi|100389047|gb|BY952251.1|BY952251
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCA-GGCT
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCT
EST: gi|208400560|gb|DC904536.1|DC904536
EST:     TTCCGNCAGATTATCGCCACATGGANGGNTTTGGTGTCC-CACCTNCAAG                         TTGATTAC-AAGGCTG
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTG
EST: gi|100385394|gb|BY950986.1|BY950986
EST:     TTCCGGCAGATTATCGGCACATGAAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAA-GAAACTTATGTAAAGT
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGT
EST: gi|162152467|gb|FC328030.1|FC328030
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
EST: gi|7067509|gb|AW497364.1|AW497364
EST:     TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAG                         TTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC
genomic: TTCCGGCAGATTATCGCCACATGGAGGGTTTTGGTGTCCACACCTTCAAGgttggttttg ... attggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggattgggcctccctatgtatgttgccattctgatgataatgtgtattggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCCACTTGTGGTGTAAAGAGCCTGTTGGATGAGGAAGCCGTTATGGTTGGAG
                            ttctgat  putative branch site (score: 3)
                                 atgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttttgataacttgttctcacacaggatttgtagacgaatttcattttttgaattctgtaaacgatctagtggggattgggcctccctatgtatgttgccattctgatgataatgtgtattggcgcagTTGATTACCAAGGCTGGCAAAGAAACTTATGTAAAGTTCCACTGGAAGCCCACTTGTGGTGTAAAGAGCCTGTTGGATGAGGAAGCCGTTATGGTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG