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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtaatacgacttgaagagatatcatttttctggtgagatgtgggctattgcattgatgtaccagtatcgatgctgacgaagccagtttgtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 11
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|208363000|gb|DC946897.1|DC946897
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162186055|gb|FC361883.1|FC361883
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|37828436|gb|BJ586448.1|BJ586448
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|18334455|gb|BJ166472.1|BJ166472
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|37844824|gb|BJ602832.1|BJ602832
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|37848287|gb|BJ606295.1|BJ606295
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|18339737|gb|BJ171764.1|BJ171764
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162191293|gb|FC366867.1|FC366867
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162158554|gb|FC334557.1|FC334557
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|37823320|gb|BJ581386.1|BJ581386
EST:     TCTCGACTGATGAAG                         AGTGCTATTGGGCAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: TCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162218504|gb|FC395081.1|FC395081
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162191294|gb|FC366868.1|FC366868
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
EST: gi|162185240|gb|FC361750.1|FC361750
EST:     ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG                         AGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC
genomic: ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAAC

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: 35 (upstream exon), 29 (downstream exon)
Score: 16

ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcct ... gtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctattgcattgatgtaccagtatcgatgctgacgaagccagtttgtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG
                           tgctgac  putative branch site (score: 16)
                                          tttgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtaatacgacttgaagagatatcatttttctggtgagatgtgggctattgcattgatgtaccagtatcgatgctgacgaagccagtttgtatttgcagAGTGCTATTGGACAGGGAATGACTCGGAAAGATCACTCCGAAGTTTCTAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA