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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaatcagctgtatgttaacagttctgaagttatgatgttttctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGACACTCCTTTGCTTACTGGACAG

Basic information

species Selaginella moellendorffii
transcript EFJ30330
intron # 8
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|169055455|gb|FE465853.1|FE465853
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169098593|gb|FE497219.1|FE497219
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169081165|gb|FE489259.1|FE489259
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169074666|gb|FE480896.1|FE480896
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169075918|gb|FE482837.1|FE482837
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169096021|gb|FE500012.1|FE500012
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169067638|gb|FE475315.1|FE475315
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169077659|gb|FE484921.1|FE484921
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169047687|gb|FE454855.1|FE454855
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169058961|gb|FE467729.1|FE467729
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169045569|gb|FE452530.1|FE452530
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169080609|gb|FE490952.1|FE490952
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169038846|gb|FE446989.1|FE446989
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169094897|gb|FE491631.1|FE491631
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169083648|gb|FE495381.1|FE495381
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
EST: gi|169026426|gb|FE435779.1|FE435779
EST:     TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAG                         ATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC
genomic: TTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGAC

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: 22 (upstream exon), 27 (downstream exon)
Score: 18

GACAAGGTTCTGGAGCTTGAATTTCAAGGTACAAAGAAGCAGTTCACTATGCTTCAGgtaatcaatc ... tctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGACACTCCTTTGCTTACTGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcaatcagctgtatgttaacagttctgaagttatgatgttttctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGACACTCCTTTGCTTACTGGACAG
                 tgttaac  putative branch site (score: 18)
                                          ttttctttatc  putative PPT
                                          ttttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaatcagctgtatgttaacagttctgaagttatgatgttttctttatcagATGTGGCCTGTCCGAACGCCACGACCTGTAGCATCTAAGCTTCCTGCAGACACTCCTTTGCTTACTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG