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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttacgctctcatcccttttcgaaatgttttctttagatatatttctagctgcccatccgttgaagacaaagtctagcgagtcttttatatgacggaatttctatattctggtgaaaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA

Basic information

species Physcomitrella patens
transcript PP1S4_12V6.1
intron # 18
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|37851638|gb|BJ609646.1|BJ609646
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162175774|gb|FC352076.1|FC352076
EST:     CTGATCCTGCCAAGATATTTGAACCCTCTGCCGAGGCGTTGGCACCTTTT                         GTGGAGGTAGCTTTAAAGCTTTTGAAAATGGAGGAGTTCACAGGCCGCTTG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|67692041|gb|BJ952274.1|BJ952274
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162178505|gb|FC354957.1|FC354957
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162276462|gb|FC452465.1|FC452465
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162263231|gb|FC439052.1|FC439052
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162231044|gb|FC406155.1|FC406155
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162180376|gb|FC355797.1|FC355797
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
EST: gi|162263230|gb|FC439051.1|FC439051
EST:     CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTT                         GTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG
genomic: CTGATCCTGCCAAGATATTCGAACCCTCTGCCGAGGCGTTGGCACCTCTTgtaagttttt ... atgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA
                                      ttttaat  putative branch site (score: 3)
                           ttttaataccatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttacgctctcatcccttttcgaaatgttttctttagatatatttctagctgcccatccgttgaagacaaagtctagcgagtcttttatatgacggaatttctatattctggtgaaaatggcaatcagctgaaaattccaccttttaataccattttaatatgattgcagGTGGAGGTAGCTTTAAAGCTTTCGAAAATGGAGGAGTTCACAGGCCGCTCGGAGCCTACAGTCATCACTTAAATATTATGCTAATGGCAAGCAGAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA