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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCACTACTTCCTCAACTCTTACAAGAACGTTCTTGCTGTGGCTCTTGCGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcctgctttccttcgttgctttgtcagtgtatgtaacgcttttctttgtttcag

Basic information

species Selaginella moellendorffii
transcript EFJ24514
intron # 4
splice site 5'
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|169059623|gb|FE468857.1|FE468857
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169109252|gb|FE512819.1|FE512819
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169035321|gb|FE443765.1|FE443765
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169053545|gb|FE463314.1|FE463314
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169053687|gb|FE461506.1|FE461506
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169075116|gb|FE484050.1|FE484050
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169103624|gb|FE506821.1|FE506821
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169114855|gb|FE516116.1|FE516116
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169078880|gb|FE489652.1|FE489652
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169040255|gb|FE448970.1|FE448970
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169060804|gb|FE469219.1|FE469219
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169035320|gb|FE443764.1|FE443764
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCC
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCC
EST: gi|169045002|gb|FE452757.1|FE452757
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
EST: gi|169102450|gb|FE503892.1|FE503892
EST:     CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAG                         GATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA
genomic: CGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAA

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), 34 (downstream exon)
Score: 55

GTCGCACTACTTCCTCAACTCTTACAAGAACGTTCTTGCTGTGGCTCTTGCGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcct ... tttgtttcagGATCCCAGTAAGTTTGCTGTGGCTGCCAGTGAAGCTCCGGCTGCGAGTGAAGCTCCGGCTGCCAAGGTTGAAGAAGAAACGAAAGCAGAGCCTGAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGCACTACTTCCTCAACTCTTACAAGAACGTTCTTGCTGTGGCTCTTGCGACCGATTACTCGTACCCTCAGGCCGAGACCGTGAAGGAGTATCTCAAGgtttgatcctgctttccttcgttgctttgtcagtgtatgtaacgcttttctttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG