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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTCCGACGGGACTCGGAGGAGACGAGAGCCAAGGAACAGGTTGCTCGTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctctcccctctttcctcttgcacgtcttagctgacaacgctctatcgttttcgtttgccag

Basic information

species Selaginella moellendorffii
transcript EFJ07199
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07199 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 5'ss of exon 1
GAAGCTCCGACGGGACTCGGAGGAGACGAGAGCCAAGGAACAGGTTGCTCGTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctctcccctctttcctcttgcacgtcttagctgacaacgctctatcgttttcgtttgccag--------------------------------
 || |     || ||  | ||||||| ||  |||||||  ||| |  ||| ||| ||||| || || ||||||||||||||||||||||||||||| | ||| ||||   | | || ||| || |      ||        | |       | | |     | |  |                                 
AAAACAATTCCGAGAGACTGAGGAGATGAAGGCCAAGGCGCAGATCTCTCATGCCCAGCCTGATGATCTCATTGATTTCTACCACCTGAAGAGCCGGAGGgtaagcttatttcactgtttgctttatagaatccacatcatccatatgtattggctaatagtgggtatcagctgtttacaaacatccaaagcttaatcaa
















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|169055889|gb|FE465103.1|FE465103
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169048126|gb|FE456841.1|FE456841
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169045183|gb|FE451416.1|FE451416
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169112255|gb|FE509971.1|FE509971
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169045184|gb|FE451417.1|FE451417
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169068317|gb|FE480714.1|FE480714
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169040227|gb|FE447096.1|FE447096
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTAAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169092859|gb|FE496323.1|FE496323
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169115539|gb|FE518048.1|FE518048
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169112256|gb|FE509972.1|FE509972
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
EST: gi|169092858|gb|FE496322.1|FE496322
EST:     GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAG                         GGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA
genomic: GTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctc ... cgtttgccagGGCATGAGCCAACTAGAGCTGGAAGACGAGGTTCAGACAGATCTGAAGCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTCCGACGGGACTCGGAGGAGACGAGAGCCAAGGAACAGGTTGCTCGTGCTCAGCCAGACGACCTCATTGATTTCTACCACCTGAAGAGCCGAAAGgttagctctctcccctctttcctcttgcacgtcttagctgacaacgctctatcgttttcgtttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA