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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgttgacgtatgcatgatttcagaattgttcagtagaatttgaacatatcactgtactttatgggatacttcaggacatgtctgtattttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGCCTCTATGGAAGATTTTCATGATACCAAAATATCAAAAGTTGATGGTATA

Basic information

species Physcomitrella patens
transcript PP1S174_123V6.1
intron # 1
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|208377763|gb|DC940875.1|DC940875
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208384917|gb|DC903424.1|DC903424
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18347357|gb|BJ179403.1|BJ179403
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGANAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208366958|gb|DC951445.1|DC951445
EST:     ACCCTTCGCAGCCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: ACCCTTCGCAG-CCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208358259|gb|DC939399.1|DC939399
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208382176|gb|DC914823.1|DC914823
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208381088|gb|DC903916.1|DC903916
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|162254449|gb|FC430662.1|FC430662
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100418751|gb|BY975722.1|BY975722
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208355611|gb|DC906591.1|DC906591
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208386792|gb|DC937184.1|DC937184
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAAAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100412818|gb|BY992451.1|BY992451
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208356189|gb|DC902225.1|DC902225
EST:     AACCCTTCGCAGCCGGAGCTGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100431608|gb|BY960283.1|BY960283
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208357765|gb|DC902303.1|DC902303
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100439819|gb|BY980255.1|BY980255
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208351894|gb|DC913793.1|DC913793
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18344474|gb|BJ176514.1|BJ176514
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208390818|gb|DC938397.1|DC938397
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18355222|gb|BJ187281.1|BJ187281
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100353890|gb|BY983361.1|BY983361
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18355314|gb|BJ187373.1|BJ187373
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18352731|gb|BJ184786.1|BJ184786
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAANAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100438994|gb|BY961907.1|BY961907
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18355100|gb|BJ187159.1|BJ187159
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100404154|gb|BY955282.1|BY955282
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|100430804|gb|BY978405.1|BY978405
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|18372532|gb|BJ204134.1|BJ204134
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
EST: gi|208377647|gb|DC932183.1|DC932183
EST:     AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAG                         TGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC
genomic: AACCCTTCGCAGCCGGAGCCGAGTGTGCCCATCAACGGAGGTGGCTTAAGgtgtgtgtct ... ttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatatcactgtactttatgggatacttcaggacatgtctgtattttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGCCTCTATGGAAGATTTTCATGATACCAAAATATCAAAAGTTGATGGTATA
                                         tatttttt  CT-rich tract
                                       tgtatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttgacgtatgcatgatttcagaattgttcagtagaatttgaacatatcactgtactttatgggatacttcaggacatgtctgtattttttggacagTGAAAACAAGAAGTTTAGCTATGGCTTTTCCAGTTTACGTGGGAAGAGGGCCTCTATGGAAGATTTTCATGATACCAAAATATCAAAAGTTGATGGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA