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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAATGCTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattctaacttcaatttgaattggcgctcaaggtcaccaattgtatagaagaagacaacgatttattgtgacaattattagaaagttcatctgaa...

Basic information

species Physcomitrella patens
transcript PP1S172_22V6.1
intron # 4
splice site 5'
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|100443039|gb|BY981665.1|BY981665
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGGAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|208376452|gb|DC902749.1|DC902749
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67717448|gb|BJ967707.1|BJ967707
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|208389492|gb|DC942199.1|DC942199
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100369785|gb|BY967385.1|BY967385
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|162174625|gb|FC350280.1|FC350280
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18347384|gb|BJ179430.1|BJ179430
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18356387|gb|BJ188446.1|BJ188446
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67718156|gb|BJ968415.1|BJ968415
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18330838|gb|BJ162844.1|BJ162844
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100353391|gb|BY964783.1|BY964783
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67716670|gb|BJ966930.1|BJ966930
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|208390428|gb|DC933685.1|DC933685
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67717265|gb|BJ967524.1|BJ967524
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100355882|gb|BY946086.1|BY946086
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100424887|gb|BY976866.1|BY976866
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67712935|gb|BJ966384.1|BJ966384
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|162229414|gb|FC405605.1|FC405605
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18366975|gb|BJ199055.1|BJ199055
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18354799|gb|BJ186857.1|BJ186857
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|208367162|gb|DC935962.1|DC935962
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18341969|gb|BJ174004.1|BJ174004
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18356942|gb|BJ189001.1|BJ189001
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100363442|gb|BY966391.1|BY966391
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18372682|gb|BJ204284.1|BJ204284
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67717486|gb|BJ967745.1|BJ967745
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|67569243|gb|BJ942067.1|BJ942067
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|18364140|gb|BJ196213.1|BJ196213
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100415505|gb|BY992875.1|BY992875
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCCCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100360303|gb|BY966108.1|BY966108
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
EST: gi|100427995|gb|BY959230.1|BY959230
EST:     CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAG                         GTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC
genomic: CTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 29 (upstream exon), 31 (downstream exon)
Score: 5

TCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAATGCTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattc ... tcgatggcagGTGGAAGCCTTCATTATCAACAATCTGAAGAGAGCTCTTACTACTCTGAACAGTTACCTTGCATCCCGGACCTACCTTGTTGGAGAATCTGTAACTCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAATGCTCGGGCGTGGGTTCTTCCTCATCTTGGGTTGGGATTCTTCAATGAAGAGgtgataattctaacttcaatttgaattggcgctcaaggtcaccaattgtatagaagaagacaacgatttattgtgacaattattagaaagttcatctgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA