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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAGAGGCAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacacttcgtaaccacttacatatatttacagtcccaccccatagtttcaagggataccaccaatctgtgggacgcgttacttgttag

Basic information

species Zea mays
transcript GRMZM2G038606_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038606_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 5'ss of exon 6
AAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAG---AGGCAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacacttcgtaaccacttacatatatttacagtcccacccca---------tagtttcaagggataccaccaatctgtgggacgcgttacttgttag
   |||||||||||||||||||| |||||||| |||||||| || ||   |||| ||||||||||||||||||| ||| |||| |  |||||||| | ||||||||  |   | |     | ||| |      || |   |||    |         | ||||  ||||  |  |||||||||      |   |   ||  ||
---CCTGGAGGCAGAGGCATTGGGCGTGGCCAGGATGATGGTGGCAGCAAAGGCGGTGGTGGCCGTGGAAGGGGAGGAATTGGAGGTAAAGGTGGCATCAAAGgtatgcttcttgcttgaatttagactctactataccgccaaagtagtttgtattttgttttgagggg-ataaccaatctgct---tgtactctatggcag
















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|211533729|gb|FL071653.1|FL071653
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|78107776|gb|DV526194.1|DV526194
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|78026896|gb|DV495283.1|DV495283
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         TGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|94474355|gb|EB703313.1|EB703313
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|31358015|gb|CD442372.1|CD442372
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|18179645|gb|BM380855.1|BM380855
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAAC-AA-                         ---AGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|211533734|gb|FL071658.1|FL071658
EST:     CAGCGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|5343007|gb|AI795312.1|AI795312
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         TGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|89252869|gb|DY624655.1|DY624655
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|84970052|gb|DW468427.1|DW468427
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|12969926|gb|BG266727.1|BG266727
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         TGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|78115516|gb|DV533904.1|DV533904
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|9952507|gb|BE639090.1|BE639090
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGCGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|78115517|gb|DV533905.1|DV533905
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
EST: gi|76927712|gb|DV171333.1|DV171333
EST:     CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTTCCAAAGGTGGTAACAAAG                         -G----TGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT
genomic: CAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacactt ... tacttgttagTGCAGGTGGGGGCCGTGGTCGTGGCTGAAGCTGGTCGACACAAGGGAGAAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCTGGAGGCAGAGGCATTGGACGTGGCCAAGATGATGGAGGTAGAGGCAGTGGTGGCCGTGGAAGGGGTGGAGTTGGTGCCAAAGGTGGTAACAAAGgtacacacttcgtaaccacttacatatatttacagtcccaccccatagtttcaagggataccaccaatctgtgggacgcgttacttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG