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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTCGGTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttatcatcaaaatatcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgatgcaattgcag

Basic information

species Glycine max
transcript GLYMA17G03540.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03540.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ35155 (Selaginella moellendorffii), 5'ss of exon 1
TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTCGGTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttatcatcaaaat--atcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgatgcaattgcag
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||| || || || || ||||||||||| |||||||||||     ||   |||| | |  |  |  |||   |       ||   | | |       | ||||  |||| | | ||      ||||  |||| |||      || |||
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagagctccatcgcgttctgaggccgcctctctcgcgcgctcttttggttttttttctt------tttttcttttctcgcaattcttccag

upper sequence: GLYMA17G03540.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ24104 (Selaginella moellendorffii), 5'ss of exon 1
TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTCGGTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttatcatcaaaat--atcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgatgcaattgcag
  | ||  | ||||| || |||||||| || ||||| ||||||||||| |||||||| ||||| ||||| || || || || ||||||||||| |||||||||||     ||   |||| | |  |  |  |||   |       ||   | | ||      | ||||  |||| | | ||      |   |||| || |             
GTTGGCCACGCTCGGGCTGTGGCAGAAGGAGGCCAAGATTCTCTTCCTAGGTCTCGACAATGCGGGGAAAACAACGCTTCTCCACATGCTCAAGGACGAGgtgagtggtttccagcttaccctagatctccatcgcgttctgaggccgcctctcttgcgcgctcttttggttttttgttttcttttctcgcaattcttccag-----------
















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|298187403|gb|HO034552.1|HO034552
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATACTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|24206013|gb|BU965266.1|BU965266
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|151393095|gb|EV262970.1|EV262970
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|19268925|gb|BM885181.1|BM885181
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|193719432|gb|FK650056.1|FK650056
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|20449793|gb|BQ253917.1|BQ253917
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|298170756|gb|HO015732.1|HO015732
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|17401176|gb|BM177958.1|BM177958
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|298167563|gb|HO012826.1|HO012826
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|26269163|gb|CA820226.1|CA820226
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|17519809|gb|BM188851.1|BM188851
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|192302890|gb|FG998572.1|FG998572
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|192298804|gb|FG988640.1|FG988640
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|298189520|gb|HO037923.1|HO037923
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|16349217|gb|BI974812.1|BI974812
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|26057414|gb|CA800328.1|CA800328
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|7925387|gb|AW831352.1|AW831352
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCAC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCAC
EST: gi|19053720|gb|BM732387.1|BM732387
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|298186789|gb|HO037422.1|HO037422
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGGATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|192332154|gb|FK024600.1|FK024600
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
EST: gi|10231278|gb|BE800157.1|BE800157
EST:     GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAG                         AGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC
genomic: GTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcc ... gcaattgcagAGATTAGTTCAGCACCAGCCGACCCAACACCCCACTTCGGAGGAATTGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAGCTTCCCTCGGTCTCTGGCAGAAAGAAGCCAAAATTCTCTTCCTCGGTCTCGATAATGCAGGGAAGACCACCCTCCTTCACATGCTCAAAGACGAGgtgaggttcctctcccttatcatcaaaatatcaaatcaaatacccttttttatttttattttttttatttttatctattaaaaagttttaattttttcgatgcaattgcag

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