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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtcatcttcttgagctttgatgaaaacaagatgtttcatttgaaaagaatgagaacaagttctgtattattgcttatagctacattggctttgatgaagtcgctgatgtcggttatctgtgacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG

Basic information

species Physcomitrella patens
transcript PP1S58_148V6.1
intron # 7
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|22491724|gb|BU051647.1|BU051647
EST:     GAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: GAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|162165067|gb|FC341621.1|FC341621
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCTAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|208390218|gb|DC949486.1|DC949486
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|162165066|gb|FC341620.1|FC341620
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCTAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|67726633|gb|BJ976892.1|BJ976892
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|67726679|gb|BJ976938.1|BJ976938
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|208374139|gb|DC952570.1|DC952570
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|22133334|gb|BQ827679.1|BQ827679
EST:     GAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: GAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|67726518|gb|BJ976777.1|BJ976777
EST:     GGAGGAGGGTGGTGCCGGAGCTTTNGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: GGAGGA-GGTGGTGCCGGAGCTTT-GGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|208362766|gb|DC950566.1|DC950566
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|162260011|gb|FC435314.1|FC435314
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|67724052|gb|BJ974311.1|BJ974311
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|162200955|gb|FC377358.1|FC377358
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCTAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|67720762|gb|BJ971021.1|BJ971021
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
EST: gi|162163441|gb|FC339975.1|FC339975
EST:     CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAG                         TTTCAAGCCTTGAGGACAATGGTTCAAGCTAATCCTCAGATTCTTCAG
genomic: CTGGAGGAGGTGGTGCCGGAGCTTTGGACTTCTTAAGAAATAACCCACAGgcatgtcatc ... gacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagctacattggctttgatgaagtcgctgatgtcggttatctgtgacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG
                         cgctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcatcttcttgagctttgatgaaaacaagatgtttcatttgaaaagaatgagaacaagttctgtattattgcttatagctacattggctttgatgaagtcgctgatgtcggttatctgtgacttggcagTTTCAAGCCTTGAGGACAATGGTTCAAGCAAATCCTCAGATTCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA