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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacacaaagttcctgtttttttcttgctctctttcctccacacatccgtgacgtgttcttagagcactttttcttttccag

Basic information

species Selaginella moellendorffii
transcript EFJ29885
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os05g01970.1 (Oryza sativa), 5'ss of exon 3
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaaga------------acacaaagttcct--------gtttttttcttgctct-ctttcctccacac-------atccgtgacgtgtt--cttag--agcac----tttttcttttccag------------------------------------------------------
||||||||||||||||||| ||||||||| ||||||||||| |             || |  | | ||        |||| |||   ||| | || | ||  | ||       |||  |||| ||||    |||  ||||       ||| |||| |||                                                      
GTGGATTGGATTGGCCAGAGGAATCAAATAGATGCTGgtaaaacatctttgtcttgcagatggattctttgaacttgtttcttttcagctatgctgttctttaaaccagtattatcaatgacttgttggtctagctagcatagctcctttttttttcagttaattcattccttgttcatgattcgtttatgttttttcgtcatcttcatgtag

upper sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os03g60740.1 (Oryza sativa), 5'ss of exon 3
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacacaaagttcctgtttttttcttgctctctttcctccacacatccgtga-cgtgttcttagagcactttttcttttccag---
||||||||||||||||| |||||||| |||||  ||||||||        |||  || || ||  |     || ||| |  |    |  || |  || |  | || | || ||   | ||  |    
GTGGATTGGATTGGCCAAAAGAATCAGATTGACACTGgtaag--------gttgttgcttattcttcttcatcattcatgtatcagtttgtaaatgtttgttaagtgaacattgcttgttttaacag

upper sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G047219_T01 (Zea mays), 5'ss of exon 3
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaac--acaaagttcctgtttttttcttgctctctttcctccaca------catccgtgacgtgttcttagagcactttttcttttccag---------------------------------------------------------------------------------------
||||||||||||||||| |||||||||||||||||||||||       |     || ||  | |   ||| |     || |   ||        |  |||      | ||  |  |||  |  |||   ||                                                                                       
GTGGATTGGATTGGCCAAAAGAATCAAATTGATGCTGgtaaatgttacccctcgtcttgcatatacgttgttacacatcataggcaacctattttttgtgctaatctgttgaactactgatcatttcaaagtgactgttgggtgaaactgcccttttttctgcaaacgtaactttctatttctgtttctcagctctttttcgttgcatttttatgcag

upper sequence: EFJ29885 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G089575_T01 (Zea mays), 5'ss of exon 2
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaac-acaaagt-tcctgtttttttcttgctctctttcctccacacatccgtgacgtgttcttagagcactttttcttttccag------------
||||||||||||||||| ||||||||||| || |||| |||     ||    | || ||  | | | ||| | | ||    |  || |  |     ||||| | |    | | | |       |             
GTGGATTGGATTGGCCAAAAGAATCAAATAGACGCTGctaaatgttaccccttgtcttgcatatatgttgatttattgaagcttcatacacaacctgtgttttcacgctaatctattaaactaatgatcatttcaac

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|169107964|gb|FE513793.1|FE513793
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169050407|gb|FE457590.1|FE457590
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169058284|gb|FE465011.1|FE465011
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169050408|gb|FE457591.1|FE457591
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|70670825|gb|DN839402.1|DN839402
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169062142|gb|FE471034.1|FE471034
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169062143|gb|FE471035.1|FE471035
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169058285|gb|FE465012.1|FE465012
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169038255|gb|FE443941.1|FE443941
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169060860|gb|FE469255.1|FE469255
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169104935|gb|FE509053.1|FE509053
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169104934|gb|FE509052.1|FE509052
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169107965|gb|FE513794.1|FE513794
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
EST: gi|169038254|gb|FE443940.1|FE443940
EST:     GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTG                         CAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA
genomic: GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAA

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: 38

GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacac ... tcttttccagCAAAAGATGCAGGTGTCAAGCACGTCGTGCTCGTCGGCTCCATGGGTGGAACCAACGAAAATCACCCCTTGAACTTACTGGGGAATGGAAAAATCCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATTGGATTGGCCAGAAGAATCAAATTGATGCTGgtaagaacacaaagttcctgtttttttcttgctctctttcctccacacatccgtgacgtgttcttagagcactttttcttttccag

- - - - - - - - - - - - - - -  ATGCTG