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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGTGAGGTATGATTTCCAGCACCTAGCTAAATGGGTCGAGCAGATCCTCCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttcttgtttttccttcgtttcttcgctctccatttctaactttgtggctttctttgtgttgaag

Basic information

species Selaginella moellendorffii
transcript EFJ19091
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19091 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 5'ss of exon 1
-GCCGTGAGGTATGATTTCCAGCACCTAGCTAAATGGGTCGAGCAGATCCTCCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttcttgtttttccttcgtttcttcgctctccatttctaa-ctttgtggctttctttgtgttgaag-----------------------------
  ||  | |||||||  | || ||  | || |  ||| |||||||||| || ||||||||| |  || ||||||| ||||||||||| |||||||||||||||||  | ||  || |    |  |     |  | |    || ||| |  |||| |||           ||                              
TACCA-GCGGTATGACGTGCACCATGTCGCGAGGTGGATCGAGCAGATACTGCCATTCTCGCTGCTGCTGCTCGTCGTCTTCATACGGCAGCATCTCCAAGgtctaatactcattctcttgtgctcgtgccattgtgtgattataagcggtgtgacttgtccaaaacaaaatcgattttccttcatgttgatgtccatata
















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|169063899|gb|FE471254.1|FE471254
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169071910|gb|FE478158.1|FE478158
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169101857|gb|FE504937.1|FE504937
EST:     CCCATTCTCGATTTTGTTACTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169110152|gb|FE513367.1|FE513367
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169060303|gb|FE467873.1|FE467873
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169056263|gb|FE464398.1|FE464398
EST:     CCCATTCTCGATTTTGTTACTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTNTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169036020|gb|FE446726.1|FE446726
EST:     CCCATTCTCGATTTTGTTACTCGTGGTCTTCATACGCCAGCATCTCCTAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169100040|gb|FE502358.1|FE502358
EST:     CCCATTCTCGATTTTGTTACTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169113565|gb|FE514476.1|FE514476
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
EST: gi|169029063|gb|FE437566.1|FE437566
EST:     CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAG                         GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC
genomic: CCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTC

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: 17 (upstream exon), 26 (downstream exon)
Score: 2

GCCGTGAGGTATGATTTCCAGCACCTAGCTAAATGGGTCGAGCAGATCCTCCCATTCTCGATTTTGTTGCTCGTGGTCTTCATACGCCAGCATCTCCAAGgtctttttct ... tgtgttgaagGTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA




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