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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtacttcattcattgaagttgatgagtcttgcattaagctatcgtggctgagtatttagggtttatttatgtgatttctggacgaatgtagtcagcacttgtaacatgtggttggccctgaaatgttaaatcaacgtttgaatctcgagggagctcaatgtgtgcactgcatttgtggattgattcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTAATCCTACCGATCCTCTGAACGGTGAAGCCGCTGCGTTGATGATGCGAGA

Basic information

species Physcomitrella patens
transcript PP1S37_166V6.1
intron # 4
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|100387203|gb|BY970347.1|BY970347
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATNCA-TGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTTACCC
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTAT-CAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTT-ACCC
EST: gi|22492750|gb|BU052673.1|BU052673
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|67696838|gb|BJ957071.1|BJ957071
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208400064|gb|DC908627.1|DC908627
EST:     AGGATCTGTATGCTTGGANGTCATCAATCAAACTNGGANTCCCATGTTCG                         ATCTTANCAATGTGTTCNAAATANTTTTGCCTCA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCA
EST: gi|162201846|gb|FC377780.1|FC377780
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|37832038|gb|BJ590050.1|BJ590050
EST:     TCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: TCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|67696647|gb|BJ956880.1|BJ956880
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162268532|gb|FC444405.1|FC444405
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162261485|gb|FC438321.1|FC438321
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162260434|gb|FC436087.1|FC436087
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162274058|gb|FC450130.1|FC450130
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208353497|gb|DC922509.1|DC922509
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208348460|gb|DC901951.1|DC901951
EST:     ANGATCTGTATGCTTGGATGTCATCAATCANACTTGNANTCCCATGTTCN                         ATCTTATCAATGTGTTCNAANTATTTTTGCCTCANCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208374764|gb|DC948694.1|DC948694
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208396037|gb|DC915797.1|DC915797
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|37851038|gb|BJ609046.1|BJ609046
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162201845|gb|FC377779.1|FC377779
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208399979|gb|DC905005.1|DC905005
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ANCTTATCAATGTGTTCNAANTANTTTTGCCTCANCTCT-ANTTTACC-TA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162274057|gb|FC450129.1|FC450129
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162222561|gb|FC398712.1|FC398712
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208361846|gb|DC950118.1|DC950118
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|37832758|gb|BJ590770.1|BJ590770
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|208378275|gb|DC918896.1|DC918896
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|37851815|gb|BJ609823.1|BJ609823
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162261484|gb|FC438320.1|FC438320
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
EST: gi|162268531|gb|FC444404.1|FC444404
EST:     AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG                         ATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA
genomic: AGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTA

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: 31 (upstream exon), 32 (downstream exon)
Score: 9

GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCGgtgagtgtac ... attcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTAATCCTACCGATCCTCTGAACGGTGAAGCCGCTGCGTTGATGATGCGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatctcgagggagctcaatgtgtgcactgcatttgtggattgattcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTAATCCTACCGATCCTCTGAACGGTGAAGCCGCTGCGTTGATGATGCGAGA
                                        gattgat  putative branch site (score: 9)
                                         attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtacttcattcattgaagttgatgagtcttgcattaagctatcgtggctgagtatttagggtttatttatgtgatttctggacgaatgtagtcagcacttgtaacatgtggttggccctgaaatgttaaatcaacgtttgaatctcgagggagctcaatgtgtgcactgcatttgtggattgattcatgcagATCTTATCAATGTGTTCGAAGTATTTTTGCCTCAGCTCTTACTTTACCCTAATCCTACCGATCCTCTGAACGGTGAAGCCGCTGCGTTGATGATGCGAGA

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