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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCACATCTCGCTCTTCAGGCTCTTGTTCCCGCCGTTCCAGAAGTACATCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaaaaaccattcctttttctttctcgatcttagagctttctctctgctaccag

Basic information

species Selaginella moellendorffii
transcript EFJ34788
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34788 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: EDP09202 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGAGCACATCTCGCTCTTCAGGCTCTTGTTCCCGCCGTTCCAGAAGTACATCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaaaaaccattcctttttctttctcgatcttagagctttctctctgctaccag--------------------------------------------------------------------------------------------------------------------------------------------
 |||||| |  |||| |||| |  | |||||||||| |||||||||||||||||||| || | |||||| ||||||||  |||||    |  | ||   |||    |  |    ||  |||    |   | |    | |      |    || || | ||                                                                                                                                            
CGAGCACGTGCCGCTGTTCAAGACCCTGTTCCCGCCCTTCCAGAAGTACATCACCAAGGGCTACGTGTCGGAGGAGGAGGCCGGCCGCCGCCTGGCAGCGgtgagtctca----cacccctgcgccccgccccggttgaagtacctgatgctactgcaaggcatctgggtctctgttaggattgtccgcagtgtttcgcgccaccgccgcacctaagggaggctgaactgaacgtacgtactattgccgcgtcttactcaagctacctcctctctgccttgctccccaacccgaccccag
















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|169055503|gb|FE465875.1|FE465875
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169078037|gb|FE487834.1|FE487834
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169059261|gb|FE467455.1|FE467455
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169070591|gb|FE479868.1|FE479868
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169051416|gb|FE457688.1|FE457688
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169081888|gb|FE486942.1|FE486942
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169053379|gb|FE460470.1|FE460470
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169022944|gb|FE428658.1|FE428658
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169067546|gb|FE475782.1|FE475782
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169096471|gb|FE498174.1|FE498174
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169031429|gb|FE437139.1|FE437139
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169100722|gb|FE503209.1|FE503209
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169099288|gb|FE501580.1|FE501580
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169099608|gb|FE501068.1|FE501068
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169069747|gb|FE477061.1|FE477061
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169106120|gb|FE507938.1|FE507938
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169046191|gb|FE456363.1|FE456363
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169037937|gb|FE446613.1|FE446613
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169041656|gb|FE449058.1|FE449058
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
EST: gi|169072102|gb|FE478714.1|FE478714
EST:     TCACTAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAG                         GTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC
genomic: TCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAAC

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: 132

AGAGCACATCTCGCTCTTCAGGCTCTTGTTCCCGCCGTTCCAGAAGTACATCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaa ... ctgctaccagGTTGTGAGAGATCCGTGCCTCCAGAAGTCCGGAGTCTACTGGAGCTGGAACAACACCTCTCAATCGTTCGAGAACACGCTGTCCGAGGAAGCCAGTGATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCACATCTCGCTCTTCAGGCTCTTGTTCCCGCCGTTCCAGAAGTACATCACCAAAGGGTTCGTGTCCGAGGAGGAATCCGGCAAGAGATTAGCTCAGgtactgcgaaaaaccattcctttttctttctcgatcttagagctttctctctgctaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA