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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcatcctcagattgcaagtgataaatactttgcaggagacggattaggagcattcctagacctttaagcttttagttcaaaatgtagacacaatttgctgatttatcctagcagaatagttatttcttctaatttttgattctttcggctttgtccgtgcttgttgatggctgtgtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATGCAAAAACTGTACTAACATTGACATCGTGATCGACTGGCTAGTGAAGCAC

Basic information

species Physcomitrella patens
transcript PP1S6_409V6.2
intron # 6
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|67699163|gb|BJ959396.1|BJ959396
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208364105|gb|DC950397.1|DC950397
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208382259|gb|DC919247.1|DC919247
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208348042|gb|DC905365.1|DC905365
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|100430815|gb|BY978411.1|BY978411
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGG
EST: gi|208391260|gb|DC933521.1|DC933521
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|162237116|gb|FC413275.1|FC413275
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|6167350|gb|AW145614.1|AW145614
EST:     GCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGNAGGTGGCATGCTACACCATTTCATG
genomic: GCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|162237115|gb|FC413274.1|FC413274
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208373818|gb|DC936589.1|DC936589
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208360397|gb|DC930778.1|DC930778
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208368100|gb|DC947660.1|DC947660
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|162264751|gb|FC440318.1|FC440318
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|162264752|gb|FC440319.1|FC440319
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAAGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|208374248|gb|DC945294.1|DC945294
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|100416820|gb|BY993105.1|BY993105
EST:     AAAATCGACNAGCCTGAGGCTATCTCANAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|162203520|gb|FC380436.1|FC380436
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
EST: gi|100417855|gb|BY975687.1|BY975687
EST:     AAATCGACAAGCCTGGAG-CTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGC
genomic: AAATCGACAAGCCTG-AGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGC
EST: gi|162203521|gb|FC380437.1|FC380437
EST:     AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAAT                         GGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG
genomic: AAAATCGACAAGCCTGAGGCTATCTCAAAGCAGGCTCTTATTGATCAAATgtaagttcat ... gtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttttgattctttcggctttgtccgtgcttgttgatggctgtgtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATGCAAAAACTGTACTAACATTGACATCGTGATCGACTGGCTAGTGAAGCAC
     tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcatcctcagattgcaagtgataaatactttgcaggagacggattaggagcattcctagacctttaagcttttagttcaaaatgtagacacaatttgctgatttatcctagcagaatagttatttcttctaatttttgattctttcggctttgtccgtgcttgttgatggctgtgtgatcacagGGACATAACAGGACTGAACGACAGGGAGGTGGCATGCTACACCATTTCATGCAAAAACTGTACTAACATTGACATCGTGATCGACTGGCTAGTGAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC