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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCCTACTTTGAGACATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagtcttggtgttatcagtgaccatcgcgtttgtgaagggagtggaatgtggagacgcaatggaactcgctgagtggaggagtggtctgactgagtgtgatgtttggcatgtggttgcag

Basic information

species Physcomitrella patens
transcript PP1S61_279V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_279V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ15497 (Selaginella moellendorffii), 5'ss of exon 6
TCCCCTACTTTGAGACATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagtcttggtgttatcagt-gaccatcgcgtttgtgaagggagtggaatgtggagacgcaatggaactcgctgagtggaggagtggtctgactgagtgtgatgtttggcatgtggttgcag
|||| ||||||||||| || ||||||||||||| |||||| || ||||| || || || || ||||| || || |||| || |||  ||||||| ||  ||| |||  |  |   ||| |||  |  | |     ||||  || |  | |                                                                             
TCCCATACTTTGAGACGTCTGCCAAGGAAGACTACAACGTAGAGGCTGCCTTTCAATGCATCGCCAAAAATGCCTTGAGGAGCGAACCGGAGGAAGACTTgtaagtttgcttgtttgtgatctttcaagcgctaagttt-cgatgtaattctcgcag----------------------------------------------------------------------

upper sequence: PP1S61_279V6.2 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ24755 (Selaginella moellendorffii), 5'ss of exon 6
TCCCCTACTTTGAGACATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagtcttggtgttatcagt-gaccatcgcgtttgtgaagggagtggaatgtggagacgcaatggaactcgctgagtggaggagtggtctgactgagtgtgatgtttggcatgtggttgcag
|||| ||||||||||| || ||||||||||||| |||||| || ||||| || || || || ||||| || || |||| || |||  ||||||| ||  ||| |||  |  |   ||| ||   |  | |     ||||  || |  | |                                                                             
TCCCATACTTTGAGACGTCTGCCAAGGAAGACTACAACGTAGAGGCTGCCTTTCAATGCATCGCCAAAAATGCCTTGAGGAGCGAACCGGAGGAAGACTTgtaagtttgcttgtttgtgatgtttcaagcgctaagttt-cgatgtaattctcgcag----------------------------------------------------------------------
















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|208361894|gb|DC953944.1|DC953944
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208389135|gb|DC945711.1|DC945711
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|100411870|gb|BY992381.1|BY992381
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGC
EST: gi|208378881|gb|DC927583.1|DC927583
EST:     TTCCAGTGTATNGCCAAGANCGCATTGAAGANCGAGACGGAGGAGGAAAT                         TTACNTGCNTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|100392311|gb|BY953300.1|BY953300
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162262618|gb|FC438439.1|FC438439
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|37829857|gb|BJ587869.1|BJ587869
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162262619|gb|FC438440.1|FC438440
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162263651|gb|FC438887.1|FC438887
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208360449|gb|DC950048.1|DC950048
EST:     AGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: AGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208362152|gb|DC954319.1|DC954319
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208387145|gb|DC941317.1|DC941317
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208374370|gb|DC948402.1|DC948402
EST:     TTCCAGTGTATTGCCAAGAACGCA-TGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|100403295|gb|BY991132.1|BY991132
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAAGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|208372735|gb|DC952622.1|DC952622
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162262701|gb|FC438483.1|FC438483
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162231219|gb|FC407006.1|FC407006
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|162231220|gb|FC407007.1|FC407007
EST:     TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
EST: gi|67695653|gb|BJ955886.1|BJ955886
EST:     TCCAGTGTATTGCCAAGGAACGCATTGAAGAACGAGACGGAGGAGGAAAT                         TTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC
genomic: TCCAGTGTATTGCCAA-GAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagt ... gtggttgcagTTACCTGCCTGATACGATCGACGTGAACGCCAGCAGGCCACAGAAAACTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCCTACTTTGAGACATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCCAGTGTATTGCCAAGAACGCATTGAAGAACGAGACGGAGGAGGAAATgtgagtcagtcttggtgttatcagtgaccatcgcgtttgtgaagggagtggaatgtggagacgcaatggaactcgctgagtggaggagtggtctgactgagtgtgatgtttggcatgtggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA