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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCAACCTCAGCCGCAAGGGCGAGGACTTCACGCTGCTCCGCGCCGACGCAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggtaacccacattgccctctgtccagcagattctaggaagtagacatcgcgttcgcctactggagttgtgtctgggatcatggacatgcggga...

Basic information

species Zea mays
transcript GRMZM2G135444_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135444_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 5'ss of exon 1
GGCCAACCTCAGCCGCAAGGGCGAGGACTTCACGCTGCTCCGCGCCGACGCAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggtaacccacattgccctctgtccagcagattctaggaagtagacatcgcgttcgcctactggagttgtgtctgggatcatggacatgcggga----------
|||    | |||||||||||| ||||||||||||||||||| |||||| || ||  ||||| || ||||||||||||||||||||||||||||||||||||||   |  |  |||    ||| | | | ||  |  ||||| | | ||     | | || |  |  | | |||||||  |||  | | | |||||  ||           
GGCGGCGCGCAGCCGCAAGGGGGAGGACTTCACGCTGCTCCTCGCCGAGGCCGGGGAGCGCGTCGCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaccgcattgccccta--tgcacgc-gccc--cgaattctggaaggt---tctagagtacctccgccg-agttgtgcgtggcctgacg-acatggaggccactcctgta
















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|148946428|gb|EC891737.2|EC891737
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211393740|gb|FL095551.1|FL095551
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|149095947|gb|EE181613.2|EE181613
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|148940139|gb|EC884892.2|EC884892
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|149101338|gb|EE187455.2|EE187455
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|149096893|gb|EE182691.2|EE182691
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211393741|gb|FL095552.1|FL095552
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211391125|gb|FL095548.1|FL095548
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211393739|gb|FL095550.1|FL095550
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|149206435|gb|ES702031.1|ES702031
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|149083526|gb|EE172858.2|EE172858
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211391126|gb|FL095549.1|FL095549
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
EST: gi|211393742|gb|FL095553.1|FL095553
EST:     CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCG                         ATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT
genomic: CAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAAT

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 3 RNA-Seq libraries.


Block sizes: 26 (upstream exon), 24 (downstream exon)
Score: 1

GGCCAACCTCAGCCGCAAGGGCGAGGACTTCACGCTGCTCCGCGCCGACGCAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAATCTGTTGAAAAACGTCTTGCGTGCCATTCCTACATGTTTCTGCAGGGAGG


Block sizes: 31 (upstream exon), 29 (downstream exon)
Score: 2

GGCCAACCTCAGCCGCAAGGGCGAGGACTTCACGCTGCTCCGCGCCGACGCAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAATCTGTTGAAAAACGTCTTGCGTGCCATTCCTACATGTTTCTGCAGGGAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 112

GGCCAACCTCAGCCGCAAGGGCGAGGACTTCACGCTGCTCCGCGCCGACGCAGGCCAGCGCATCCCCGGCGACCCGTCCACCTCCTTCTCCGTCTTCGCGgtaagtcggt ... tgattgctagATTTTTGATGGGCACAACGGATCAGGAGCTGCCATATACGCAAGGGAGAATCTGTTGAAAAACGTCTTGCGTGCCATTCCTACATGTTTCTGCAGGGAGG