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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccctggttcccttgcttcatgacatgtactattttttattaccactgtcatctcttaactggctattttattccaccctgattgctgcctgtgcag

Basic information

species Zea mays
transcript GRMZM2G120578_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g15550.2 (Oryza sativa), 5'ss of exon 2
CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgc--ccctggt-tcccttgcttcatgacatgtactattttttattaccactgtcatctcttaactggctattttattccaccctgattgctgcctgtgcag
||||||||||||||||| || ||||||||||| || || |||||||||||||| ||||||||||| || ||||||||||||||||| || || | | |||||| |   |  || | |  |||| ||| |||     || ||   |  ||    |  |  | |      ||   || ||  |    |   |||   |  |||||||
CCTTGCTGCGTCAAGGCCAGGGCGGCGGCGCCTGAATCCGAGGCCAAGTGCCACGCCACCGTGGTGTCCGGATGGTTCACCGAGCCCCGCTCGCGCGGCGgtatgtgacgttgttgtttcttgattcttgatgatgacgatagatgctttatgccctattttggatgatgatgatgttcgtttgtctgaattttggtttgtgcag
















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|211320667|gb|FL013191.1|FL013191
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|148956445|gb|EC902269.2|EC902269
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|78117805|gb|DV536192.1|DV536192
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|148931937|gb|EC875166.2|EC875166
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|148930370|gb|EE284813.2|EE284813
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|211322828|gb|FL013194.1|FL013194
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACAATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|149072878|gb|EE161134.2|EE161134
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|211320668|gb|FL013192.1|FL013192
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTG
EST: gi|211322835|gb|FL013201.1|FL013201
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|89756410|gb|DY686460.1|DY686460
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|211322829|gb|FL013195.1|FL013195
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|32865849|gb|CF005531.1|CF005531
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|28188224|gb|CB179834.1|CB179834
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|211322831|gb|FL013197.1|FL013197
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
EST: gi|148963955|gb|EE015081.2|EE015081
EST:     CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCG                         GTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG
genomic: CCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG

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: 242

CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 251

CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

CCTTGCTGCGTCAAGGCGAGAGCGGCGGCGCCCGAGTCTGAGGCCAAGTGCCATGCCACCGTGGTTTCGGGATGGTTCACCGAGCCACGATCACACTGCGgtacgcccct ... gcctgtgcagGTAAAGCCAGCAAGGTTCAGTATTACAATAACCCAATGTGGCCAG