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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataacagtctgtctgataatattccaaacgcacttgctttacaagtatctacataactaagttactcagggcgaggattcatccctatcggaat...

Basic information

species Physcomitrella patens
transcript PP1S21_362V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S21_362V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP05500 (Chlamydomonas reinhardtii), 5'ss of exon 3
CGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataacagtctgtctgataatattccaaacgcacttgctttaca-agtatctacataactaagttactca---gggcgaggattcatccctatcggaat
                     ||||| ||||||||||| |||||| |||| ||||||||||| || |||||||||||||| ||||| || || || || |||  | |    |  ||| |      || |    |    |  |     || || | || |         ||   ||   || ||  ||    |  | |  |    
---------------------GTGACCCAGGTGCGCGTCAAGTTCCTGGACGACCAGAACCGCCTGATCATGCGCAACGTGAAGGGCCCCGTCCGCGAGGgtgagcacgcga--ctgccccgcgctagtatggagctgcccggagggcagagcagcttcggggagccctttgccaactggacggagaggggtgtcgacagcg--

upper sequence: PP1S21_362V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ30111 (Selaginella moellendorffii), 5'ss of exon 2
CGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataacagtctgtctgataatattccaaacgcacttgctttacaagtatctacataactaagttactcagggcgaggattcatccctatcggaat
 | || || || || ||||| ||||| || || || || |||||| |||| |||||||| ||||||||||||||||| |||||||||||  | || ||||||| |  |  |  ||     |||   ||   | |   |    ||||     ||  | | |   ||                                   
AGGACGGGATCTCGCGGGCAAGTGACCCAAGTCCGGGTGAAGTTCCTGGACGACCAGAATCGTCTCATCATGCGCAATGTCAAGGGGCCGATCCGCGAAGgtaagc-tctcgatcctctcgatcgaatcgaagattgat---ctttggggctaatttcttgtgtag----------------------------------

upper sequence: PP1S21_362V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ08290 (Selaginella moellendorffii), 5'ss of exon 2
CGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataacagtctgtctgataatattccaaacgcacttgctttacaagtatct-acataactaagttactcagggcgaggattcatccctatcggaat
 | || || || || ||||| ||||| || || || || |||||| |||| |||||||| ||||||||||||||||| |||||||||||  | || ||||||| |  |  |  ||     |||   ||   | |   |  |      ||| | |||    ||                                       
AGGACGGGATCTCGCGGGCAAGTGACCCAAGTCCGGGTGAAGTTCCTGGACGACCAGAATCGTCTCATCATGCGCAATGTCAAGGGGCCGATCCGCGAAGgtaagc-tctcgatcctctcgatcgaatcgaagattgatctttggggcaaatttcttgtgtag--------------------------------------

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|162205567|gb|FC381834.1|FC381834
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162191903|gb|FC366908.1|FC366908
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162205553|gb|FC381833.1|FC381833
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162200856|gb|FC377051.1|FC377051
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|18367866|gb|BJ199949.1|BJ199949
EST:     TGGCCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|37848412|gb|BJ606420.1|BJ606420
EST:     TGGCCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|18369526|gb|BJ201613.1|BJ201613
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|67723437|gb|BJ973696.1|BJ973696
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162199653|gb|FC375892.1|FC375892
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162228654|gb|FC405474.1|FC405474
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|19788839|gb|BQ040954.1|BQ040954
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|37827391|gb|BJ585403.1|BJ585403
EST:     GACCAGAACCGTCTCATCCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGG
genomic: GACCAGAACCGTCTCAT-CATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGA-CCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGG
EST: gi|162250020|gb|FC427121.1|FC427121
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|19776818|gb|BQ039116.1|BQ039116
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162233115|gb|FC408938.1|FC408938
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|18331708|gb|BJ163719.1|BJ163719
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162191902|gb|FC366907.1|FC366907
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|67709361|gb|BJ965177.1|BJ965177
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162248540|gb|FC425316.1|FC425316
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162265173|gb|FC441260.1|FC441260
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162252421|gb|FC427815.1|FC427815
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162252422|gb|FC427816.1|FC427816
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162220650|gb|FC396862.1|FC396862
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|37850839|gb|BJ608847.1|BJ608847
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|162278394|gb|FC454480.1|FC454480
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCAAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGA
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|18335239|gb|BJ167257.1|BJ167257
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
EST: gi|18348022|gb|BJ180069.1|BJ180069
EST:     TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAG                         GTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT
genomic: TGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGT

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), 35 (downstream exon)
Score: 79

CGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGAACCGTCTCATCATGCGCAACGTCAAGGGGCCAGTGCGAGAAGgtatgtataa ... ttgtttgtagGTGACATCTTGACCCTTCTTGAGTCCGAGCGCGAAGCCCGGAGGCTGCGGTGAGGAGAAACAGTCTCCCGGTGCTCTGAAGCTTGATTTGCTGTGCATGT




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