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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccctgttcttttatcattcgttctttctttctttttaatgcttacccttgcttgcttgctctttcttggcggatgcatgcag

Basic information

species Zea mays
transcript GRMZM2G097768_T01
intron # 2
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 2
lower sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 1
CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaa--------cccctgttcttttatcattcgttctttctttctttttaat--------gcttacccttgcttgct-tgctctttcttggcggatgcatgcag
||| ||||| || || |||||||||||||| ||||| || |||| |||||| ||||| ||||||||||||||  | ||||| |||||| ||||||| |||||||          | || |||| ||    |    |  || |  ||  |||||          || |  ||  ||||| ||    ||||  ||    || |||||
CATCGTCGCCCTCGGCCCCATCCAGTTCGGCTTCACCTGCGGCTTCTCCTCGCCCACCCAGGACGCCATCATCTCCGACCTCGGCCTCACCCTCTCCGAGgtgaggcaagctctctctcttctcttggagtatcatgcttatgcctaattaatcttatcggatttgcgtttaattgctctgtctcttctctgctcgcgc-tgcag
















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|6601696|gb|AW256092.1|AW256092
EST:     NGCCCACGCAGGACGCCATCATTGCTGATCTCGGCCTCTCCCTCTCTGAG                         NTCTCCCTTTTCGGNTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|211276578|gb|FL135686.1|FL135686
EST:     CGCCCACGCAGGACGCCATCATTGCTGATCTCGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|101389587|gb|EB816726.1|EB816726
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAAGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|50325333|gb|CO520459.1|CO520459
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|148987704|gb|EE031592.2|EE031592
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|71766862|gb|DR964799.1|DR964799
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|211019851|gb|FL284293.1|FL284293
EST:     CGCCCACGCAGGACGCCATCATTGCTGATCTCGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGAT
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGAT
EST: gi|50325566|gb|CO520692.1|CO520692
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|148964510|gb|EC905855.2|EC905855
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|71331313|gb|DR802490.1|DR802490
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|211126451|gb|FL284306.1|FL284306
EST:     CGCCCACGCAGGACGCCATCATTGCTGATCTCGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|148991896|gb|EE033498.2|EE033498
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|211126444|gb|FL284299.1|FL284299
EST:     CGCCCACGCAGGACGCCATCATTGCTGATCTCGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
EST: gi|148958173|gb|EC904377.2|EC904377
EST:     CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAG                         TTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC
genomic: CACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATC

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: 130

CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG


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

CATTGTCGCGCTAGGTCCCATCCAGTTCGGTTTCACATGTGGCTACTCCTCACCCACGCAGGACGCCATCATTGCTGACCTTGGCCTCTCCCTCTCTGAGgtgaacccct ... atgcatgcagTTCTCCCTCTTCGGTTCATTATCTAATGTAGGGGCGATGGTAGGCGCCATCTCCAGTGGGCAACTTGCAGAGTATATCGGCCGCAAGGGG