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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGGAATCGTCCGTATTCAGCGCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttctcctttcttcgtgtgtgctagctctttgatcgtttcgtgctcgaatcctcacag

Basic information

species Selaginella moellendorffii
transcript EFJ27946
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27946 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA01G41620.2 (Glycine max), 5'ss of exon 2
CGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGGAATCGTCCGTATTCAGCGCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaa--aatttctcctttcttcgtgtgtgctagctctt---------tgatcgtttcgtgctcgaatcctcacag-------------------------
 ||  | |||||||||||| | ||||  ||    || || ||| |     |  | || ||||||||||| ||||||||| |||| |||||||| |||||||| |  ||||| |  ||  |||       ||   | ||         | ||    | |   ||   || |                              
GGTGAGGTGCTGGGAGTATAGGCAGCAACCTTCCATTGTTCGTTTGACAAGGTCTACCCGCCCTGACAAGGCTCGTCGCTTGGGCTTCAAGGCTAAGCAGgttaacaatttgtttttctttctcacaatcttattgttaccgaatactaatttactagcattcatttctttttcaaattactgtgtactttgtgagttgt

upper sequence: EFJ27946 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S7_364V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGGAATCGTCCGTATTCAGCGCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgta-----aaatttct---cctttcttcgtgtgtgctagctctttgatcgtttcgtgct-cgaatcctcacag---------------------------
 || ||||||||||||||  | || || ||||| || || ||| |    || ||  ||||||||||||| ||||| |||||||||| |||||| || ||||||     ||| ||      ||||   |    || ||   |  |||  |   | ||  |  |||      ||                            
TGTGCGCTGCTGGGAGTACAGACAACTACCCGGCATTGTACGTGTCACTCGTCCTTCTCGCCCTGACAAGGCTCGACGCCTGGGATACAAGGCGAAACAGgtatgttcaaacttgcgaatctttaacctacagtactttttgcttgggcaggttgtagtatgaactgcggcaagtgcatcgctttgactggtgggtaatc
















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|169047288|gb|FE456537.1|FE456537
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169058518|gb|FE464244.1|FE464244
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169058894|gb|FE468728.1|FE468728
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169070557|gb|FE479834.1|FE479834
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169063696|gb|FE471802.1|FE471802
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169101168|gb|FE501925.1|FE501925
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169109682|gb|FE511754.1|FE511754
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169101169|gb|FE501926.1|FE501926
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169109683|gb|FE511755.1|FE511755
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169073901|gb|FE482991.1|FE482991
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169021073|gb|FE430682.1|FE430682
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169038352|gb|FE443986.1|FE443986
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169038351|gb|FE443985.1|FE443985
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169058895|gb|FE468729.1|FE468729
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169021074|gb|FE430683.1|FE430683
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|70670086|gb|DN838663.1|DN838663
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169096233|gb|FE497819.1|FE497819
EST:     CGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: CGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169096234|gb|FE497820.1|FE497820
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169047289|gb|FE456538.1|FE456538
EST:     GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169073900|gb|FE482990.1|FE482990
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169058517|gb|FE464243.1|FE464243
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
EST: gi|169070556|gb|FE479833.1|FE479833
EST:     GCCCGACGCGCCCTGACAAGGCTCGTCGCCTGGGATTCAAGGCCAAGCAG                         GGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA
genomic: GCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCA

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: 43

CGTCCGCTGCTGGGAGTATCGCCAGCTCCCCGGAATCGTCCGTATTCAGCGCCCGACTCGCCCTGACAAAGCTCGTCGCCTGGGATTCAAGGCCAAGCAGgtaaaatttc ... atcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTCTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC




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