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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaagcaccaaaaatttttacgcaactttgccaactttttatctcttttccgcag

Basic information

species Selaginella moellendorffii
transcript EFJ25874
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25874 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G127338_T01 (Zea mays), 5'ss of exon 3
GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaagcaccaaaaatttttacgcaactttgccaactttttatctcttt-tccgcag--------------------------------
  ||| |  |||| |||||    |||||  |  | ||||||||||| |||||| |||||||| |||| |||||| | || || ||||||||||| ||  |||  |     |   |     | | ||   |  | |  |    |  |  |  |   | |||                                  
TCATCATGATCTTCGCCTCCTGCCACTTGGTGCTCTCCCAGCTCCCCAACTTCCACTCCATCTCCGGCGTCTCCCTCGCCGCCGCCGTCATGTCGCTTTGgtgggttcccgt-tcgttcctctctatatatatatatctctgtcatgcccatgcgtacgccaacaccactgatatatatatatgcttgttgcag

upper sequence: EFJ25874 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA19G22590.1 (Glycine max), 5'ss of exon 3
GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaagcaccaaaaatttttacgcaactttgccaactttttatctcttttccgcag-----------------------------------------
  ||  |  |||||||||| ||||||||  |  ||||||| |||||  ||||||||||||| || || || |||||||||||||| ||||||||  | |||||  |        | |   | | ||   |  |||| |||  || ||| | |  ||| |                                           
TCATTATGATCTTTGCCTCTGTTCACTTTGTACTGTCCCATCTCCCTGACTTCAACTCCATTACTGGTGTATCCTTGGCAGCAGCAGTCATGTCCTTAAGgtacaagcctctttccat--tctatataaacttttggcaaaattatatttttggtcccccattttattttgaatttcagatttggtcctcggtaaattaatt

upper sequence: EFJ25874 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA16G06740.1 (Glycine max), 5'ss of exon 2
GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaagcaccaaaaatttttacgcaactttgccaactttttatctcttttccgcag------------------------------------------
  ||| |  ||||||| || ||||| ||  || | || || || || ||||||||  ||||| | ||| |||||||||| |||||  ||||||||||||||||| |  |  || |||      |||  || |  |     || || || | ||||     |                                          
TCATCATGATCTTTGCTTCTGTTCATTTTGTCCTCTCTCACCTTCCCAACTTCAATGCCATCTCTGGAATCTCCTTGGCTGCAGCAATCATGTCTCTCAGgtaa-attagtcaacaagttaacttaaccagccctctt--ctattaattttttttttaaggctcttctattaatttatatgtctttttcatttcttttatact

upper sequence: EFJ25874 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT1G25530.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaagcaccaaa------aatttttacgcaactttgccaactt--tttatctcttttccgcag-------------------------------
||||||||| ||| |    ||| || ||| |  | ||||||||||| |||||||||||| |  ||||||||||| |||| || ||||||||||||||| ||| |     | ||||  |       | | |||    ||  ||   | |    |||    || |    ||                               
GGATCCTCGGCTTCGGTGGAGTCCATTTCATTCTCTCCCAGCTCCCTAACTTCAACTCCGTTGCCGGAGTCTCCCTGGCTGCCGCCGTCATGTCTCTCTGgtcactctcaccaccttatcaccacaatattattttaccgtgttgaatcaacttaaaatttgttaagagatcgtattttcagtttttggaaaaacatgac

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|169100469|gb|FE502683.1|FE502683
EST:     TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAG                         TTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGCCAA-AAGCAAA
genomic: TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaa ... ttttccgcagTTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGCCAAGAAGCAAA
EST: gi|169053550|gb|FE463319.1|FE463319
EST:     TTCAACTCAATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAG                         TTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGCCAAGAAGCAAA
genomic: TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaa ... ttttccgcagTTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGCCAAGAAGCAAA
EST: gi|169083876|gb|FE492788.1|FE492788
EST:     TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAG                         TTACTCGACGATTGCATGGGTTGCTCCAGTGCATTA
genomic: TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaa ... ttttccgcagTTACTCGACGATTGCATGGGTTGCTCCAGTGCATTA
EST: gi|169072771|gb|FE484349.1|FE484349
EST:     TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAG                         TTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGGCCA-GAAGC
genomic: TTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaa ... ttttccgcagTTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGG-CCAAGAAGC

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: 34 (upstream exon), 34 (downstream exon)
Score: 23

GGATCCTCGTCTTTGCCTCAGTTCACTTCTTCTTGTCCCAGCTCCCAAACTTCAACTCCATCACCGGAGTCTCCTTGGCAGCAGCCGTCATGTCTCTCAGgtaagaagaa ... ttttccgcagTTACTCGACGATTGCATGGGTTGCTCCAGTGCATTACGGCCAAGAAGCAAAGCCACCAATGACCAAAGTGAGCTACGCTTATCCTCACTCTCCATCAGTG




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