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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAGCTGCAGCTTTCTCGAAGTTGACTGTACAGGATTTGAGGAAGCTCATCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttctgcctattcttgcagccaacccttatgttgtgcaacactgctgctactgatactctttgtttttaacctgtgcag

Basic information

species Zea mays
transcript GRMZM2G049347_T01
intron # 2
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|211006823|gb|FL318408.1|FL318408
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATG-CTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|211319263|gb|FL042436.1|FL042436
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|148948354|gb|EC893872.2|EC893872
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|149108271|gb|EE292611.2|EE292611
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|148933622|gb|EC877505.2|EC877505
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|211319255|gb|FL042428.1|FL042428
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAA
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAA
EST: gi|149096357|gb|EE182083.2|EE182083
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|148971875|gb|EE022637.2|EE022637
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|149000007|gb|EE037098.2|EE037098
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|211319262|gb|FL042435.1|FL042435
EST:     TCCCTCCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
EST: gi|149060778|gb|EE157228.2|EE157228
EST:     TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAG                         CTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG
genomic: TCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 119

TACAGCTGCAGCTTTCTCGAAGTTGACTGTACAGGATTTGAGGAAGCTCATCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 111

TACAGCTGCAGCTTTCTCGAAGTTGACTGTACAGGATTTGAGGAAGCTCATCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 93

TACAGCTGCAGCTTTCTCGAAGTTGACTGTACAGGATTTGAGGAAGCTCATCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 171

TACAGCTGCAGCTTTCTCGAAGTTGACTGTACAGGATTTGAGGAAGCTCATCCCACCCGAGTTTTATCCATCATGGGTTTCATTCACACAAAAGCAGAAGttgagtttct ... acctgtgcagCTTAAATGGCTGAATCAAGAGCTGACAAAAATCTGGCCATTTGTCAATGAG