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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttcttgtagcccatggatcatttcttgcacacagcgccgcctcacacgttaccaaaaccaaacatgtatgtgttccattccatccag

Basic information

species Zea mays
transcript GRMZM2G123029_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123029_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g04630.6 (Oryza sativa), 5'ss of exon 9
CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttcttgtagcccatggatcatttcttgcacacagcgccgcctcacacgttaccaaaaccaaacatgtatgtgttccattccatccag----------
|||||| ||||| ||||| |||||||||||  | ||||| |||||||| |  ||||| |||||||| ||||||||||| || |  || |||||  ||||||| | |  | ||  | | | | ||||||     | |    | ||  ||      |  ||  |    |  ||| |  | |  |||   |  |           
CCCCAATGGAGAATCAACTGTCAGCTGCCATCAAATCTCGAAGATGCCTAATCTTGCATTCACCATTGCAAACAAGACATTTATTCTTACACCAGAGCAGgttcgtgatagtctctcctagctcattttgccaatatta-gtcgggtctttttctttcagcatggtat-tgttttaggtaaatttttttgacgcatttgttt
















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|211417811|gb|FL246180.1|FL246180
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|149100422|gb|EE186497.2|EE186497
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|78021643|gb|DV490030.1|DV490030
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|110208372|gb|EC890269.1|EC890269
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|14244924|gb|BG842862.2|BG842862
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|148999547|gb|EE036519.2|EE036519
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211114340|gb|FL479352.1|FL479352
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|32913325|gb|CF018137.1|CF018137
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|7204603|gb|AW559186.1|AW559186
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|149078277|gb|EE167036.2|EE167036
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211417815|gb|FL246184.1|FL246184
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|93012558|gb|EB638078.1|EB638078
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|13515812|gb|BG518088.1|BG518088
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|16927660|gb|BM080729.1|BM080729
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTATGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211453148|gb|FL447178.1|FL447178
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|6827002|gb|AW330645.1|AW330645
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|32859335|gb|CD999016.1|CD999016
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|45567994|gb|CK985848.1|CK985848
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|78109241|gb|DV527657.1|DV527657
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACCCCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|149097402|gb|EE183255.2|EE183255
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|40303709|gb|CK348096.1|CK348096
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|6993891|gb|AW453105.1|AW453105
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|148980773|gb|EE027343.2|EE027343
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|18180292|gb|BM381502.1|BM381502
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211489971|gb|FL475496.1|FL475496
EST:     GCTTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|149066691|gb|EE286828.2|EE286828
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|110520668|gb|EE024852.1|EE024852
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211453149|gb|FL447179.1|FL447179
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|211401889|gb|FL450336.1|FL450336
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|60358971|gb|DN225944.1|DN225944
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|6695716|gb|AW288794.1|AW288794
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCGAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|5510772|gb|AI857156.1|AI857156
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|91876727|gb|EB406684.1|EB406684
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|91876845|gb|EB406802.1|EB406802
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|110943954|gb|EE164111.1|EE164111
EST:     GCCTGGGGTTCGCCATCGCAAGCAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
EST: gi|148987680|gb|EE031561.2|EE031561
EST:     GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAG                         TACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC
genomic: GCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTC

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: 206

CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTCATGGCGTATGACGTGCCACCGCCGCGTGGTCCTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2124

CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTCATGGCGTATGACGTGCCACCGCCGCGTGGTCCTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1917

CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTCATGGCGTATGACGTGCCACCGCCGCGTGGTCCTCTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2067

CCCCAACGGAGAGTCAACAGTCAGCTGCCAGGAGATCTCCAAGATGCCCAGCCTTGCGTTCACCATCGCAAACAAGACCTTCACCCTAACACCCCAGCAGgtgctttctt ... ttccatccagTACATTGTGAAGCTGGAGCAAGGAGGCCAAACCGTCTGCATCAGTGGGTTCATGGCGTATGACGTGCCACCGCCGCGTGGTCCTCTCTG