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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactaccaccttactttgtctttgctagatcatgaatcgcaatgcaatacgactgacttaatcattgtttaagtgtgcatagcatccatactatataggaggcttcgctgctttgctaattggaaccttgaaagatatgcctgtgatgatttttcagaccgatggactgattgaattatttgtttggccttgtag

Basic information

species Zea mays
transcript GRMZM2G097768_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097768_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 2
TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactaccaccttactttgtctttgctagat-catgaatcgcaatgcaat-acgactgac-ttaatcattgtttaagtgtgcatagcatccatactatataggaggcttcgctgctttgctaattggaaccttgaaagatatgcctgtgatgatttttcagaccgatggactgattgaattatttgtttggccttgtag
||||| || ||||| ||  | || || || ||||| ||||| ||||||||| |||| || ||  | || ||||| |||||||||||||||||||| || || |  | | |||   |||  |  |   |  ||| | |     |  ||  |    || | | || |  |  ||  |  || | ||  |   |                                                                                                     
TTCTCGCTGTTCGGGTCGCTGTCGAACGTCGGGGCAATGGTGGGCGCCATCGCCAGCGGCCAGATCGCCGAGTACATCGGCCGCAAGGGGgtgagcct-ccgctgtcccttgctcttgacacttgtctagatcacgacatttttgcggttactgtttagcgttttccatatgaacggagaaaccggatcgt-----------------------------------------------------------------------------------------------------
















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|101389587|gb|EB816726.1|EB816726
EST:     TAAGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGGAAGGGG                         GCTCTCTTGATCGCTGCGATTCCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCA
EST: gi|50325333|gb|CO520459.1|CO520459
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|148987704|gb|EE031592.2|EE031592
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|71766862|gb|DR964799.1|DR964799
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|50325566|gb|CO520692.1|CO520692
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|148964510|gb|EC905855.2|EC905855
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|71331313|gb|DR802490.1|DR802490
EST:     AGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCCGCA-GGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATC
genomic: AGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCC-GCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATC
EST: gi|211126451|gb|FL284306.1|FL284306
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGAT-CCAAAACATAA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAA-CATAA
EST: gi|148991896|gb|EE033498.2|EE033498
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAAAATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
EST: gi|211126444|gb|FL284299.1|FL284299
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGC
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGC
EST: gi|148958173|gb|EC904377.2|EC904377
EST:     TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG                         TCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA
genomic: TAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCA

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGGgtgagactac ... ggccttgtagTCTCTCATGATCGCTGCGATTCCAAACATAATTGGGTGGCTCGCGATATCATTTGCAAAA