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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattcttcttcttcttctcgtctcgtgcttccatctcactatttccattccaacttgatccttatccatccagacacggatgttcgttccaaagctgacctttctccccgccacgtgttcttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG

Basic information

species Zea mays
transcript GRMZM2G080375_T02
intron # 2
splice site 3'
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|74234373|gb|DT642287.1|DT642287
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|211522284|gb|FL320492.1|FL320492
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|148940563|gb|EC885365.2|EC885365
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|211143668|gb|FL321938.1|FL321938
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|149076118|gb|EE164702.2|EE164702
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|148941151|gb|EC886025.2|EC886025
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|18661967|gb|BM501673.1|BM501673
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|76914829|gb|DV165709.1|DV165709
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|37416938|gb|CF646120.1|CF646120
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|76290797|gb|DV030365.1|DV030365
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|149069151|gb|EE157880.2|EE157880
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGGCAA                         GCAGTATTTCGTCCACCCAGACGACACCGTCACGCACAAGATT
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAGATT
EST: gi|149111238|gb|EE294735.2|EE294735
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|76913985|gb|DV165359.1|DV165359
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|78078027|gb|DV506442.1|DV506442
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
EST: gi|148935767|gb|EC879810.2|EC879810
EST:     ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAA                         GCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
genomic: ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG

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), 44 (downstream exon)
Score: 34

ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 252

ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 273

ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 57

ACATACCCGAATCCTCTCCAAGACAACCCGGCGTATTCAGTCGTCAAgtatgaattc ... ttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggatgttcgttccaaagctgacctttctccccgccacgtgttcttcctcccagGCAGTATTTCGTCAACCCAGACGACACCGTCACGCAGAAG
                 agctgac  putative branch site (score: 57)
                       cctttctccccgccac  CT-rich tract