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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGCGGATGCGCCGGTCTTCGATTACCGCTCCACCGCAGGCGGCAACGGGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccgtgacgctccttttcttcttcttgacttgattcttcatcggagaacgaggcgcttggatcggtgctgtggctgggttcgtgtgtaggatta...

Basic information

species Zea mays
transcript GRMZM2G069816_T01
intron # 1
splice site 5'
intron type U2

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|78092729|gb|DV521103.1|DV521103
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|37385479|gb|CF629884.1|CF629884
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGAAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACTAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|148948792|gb|EC894194.2|EC894194
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|211397568|gb|FL031684.1|FL031684
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|149097331|gb|EE183163.2|EE183163
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|78104074|gb|DV522492.1|DV522492
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|211397570|gb|FL031686.1|FL031686
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTYTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
EST: gi|149096648|gb|EE182414.2|EE182414
EST:     GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAG                         AGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG
genomic: GGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTG

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), 47 (downstream exon)
Score: 95

GTCGGCGGATGCGCCGGTCTTCGATTACCGCTCCACCGCAGGCGGCAACGGGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTGAGGCGTGCAGACAGAGAGGACAGCGTTAGGCGAACTGTTTATGTCTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

GTCGGCGGATGCGCCGGTCTTCGATTACCGCTCCACCGCAGGCGGCAACGGGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTGAGGCGTGCAGACAGAGAGGACAGCGTTAGGCGAACTGTTTATGTCTCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 152

GTCGGCGGATGCGCCGGTCTTCGATTACCGCTCCACCGCAGGCGGCAACGGGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTGAGGCGTGCAGACAGAGAGGACAGCGTTAGGCGAACTGTTTATGTCTCTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 116

GTCGGCGGATGCGCCGGTCTTCGATTACCGCTCCACCGCAGGCGGCAACGGGGCCACCGACGATCCCTTTTACGTTGGGTTTGGGAACCAGCAGCGCAAGgtatgatccg ... ccatcttcagAGAGGGAATGGATACATCAACCAAGGAAGGAGGAGGACAAATGATAGGTTGAGGCGTGCAGACAGAGAGGACAGCGTTAGGCGAACTGTTTATGTCTCTG