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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcctacctcttacttttgttatgctttatgtgagtcatgtctgttaaaaacaacttaggaggaactaagtgtcttcgatattaagaaagaaatt...

Basic information

species Zea mays
transcript GRMZM2G147450_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147450_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct------acctcttacttttgttatgctttatgtgagtcatgtctgttaaaaacaacttaggaggaactaagtgtc--ttcgatattaagaaagaaatt
 || |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||| ||||| || || ||||| ||||| |||||||||||||| ||||||||||      || ||||||| || | || ||  ||| || |||||| | || |        | |  |||| ||    ||  || ||  || || |  |    
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgac-----tctcgagggaaatagccttccgtttgaatttcagtacaat---

upper sequence: GRMZM2G147450_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcctacctcttacttttgttatgctttatgtgagtcatgtctgttaaaaacaacttaggaggaactaagtgtcttcgatattaagaaagaaatt--
|||  | || || || || ||||| |||||||||||||||||||| || ||||| |||||  || | || || | ||| |  || || || ||||| ||||| |||   ||  |   |||||| || | |  ||  |   | ||   | ||   |             | |  |   | |   | ||  |  ||    ||  
GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatgg-acttttcttctacactaattctttgataaat-tttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag
















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|22552626|gb|BU102465.1|BU102465
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21626214|gb|BQ621135.1|BQ621135
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|148969715|gb|EE020587.2|EE020587
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|6021531|gb|AW066459.1|AW066459
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|211486296|gb|FL444470.1|FL444470
EST:     TGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: TGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20301382|gb|BQ164325.1|BQ164325
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|37392466|gb|CF633484.1|CF633484
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20802593|gb|BQ293643.1|BQ293643
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|148934461|gb|EC878500.2|EC878500
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|45846984|gb|CN070927.1|CN070927
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATTAGTGCACAG                         AGCCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|20208474|gb|BQ134563.1|BQ134563
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCCCAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|5670854|gb|AI932117.1|AI932117
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|211122171|gb|FL463027.1|FL463027
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGTAGAAGTH
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21760053|gb|BQ635594.1|BQ635594
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|149102853|gb|EE288195.2|EE288195
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|21759841|gb|BQ635382.1|BQ635382
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|74245055|gb|DT652969.1|DT652969
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
EST: gi|78544147|gb|DV621645.1|DV621645
EST:     ATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAG                         AACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA
genomic: ATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 136

GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 193

GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 187

GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct ... ttccatgtagAACCATAACTACGCAGTTGACCCAGAATCACTTCCAGAAGGAGCAGAAGTAACTCACGTCAATCTCAACGACAATAGTTGTGCTGGCCTTCAGTACGCCA