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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAATAAAGAGGAAAATTGAACAAGCAGCAACATCTGATTTTCAGGCGCGTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaatctgccctttgttgcaagtcgcaagtaagctaaattttgtggtatcatgtgttcttactgactcttcttctgtgttgtag

Basic information

species Zea mays
transcript GRMZM2G005737_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005737_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g01840.1 (Oryza sativa), 5'ss of exon 6
GGCAATAAAGAGGAAAATTGAACAAGCAGCAACATCTGATTTTCAGGCGCGTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaatctgccctttgttgcaagtc-------gcaagtaagctaaattttgtggtatcatgtgttcttactg---actcttcttctgtgttgtag--
|||||||||||||||||||||||| |||||||||||||| ||||||  ||||||||| ||  ||||||| |||||||| |||| ||| || |||||||| |||||| ||||   | ||| ||  |  |        || ||  || |  || ||    | |||| || |   | |    ||    |||      | | |  
GGCAATAAAGAGGAAAATTGAACAGGCAGCAACATCTGACTTTCAGATGCGTAGCTTACCCACCAAACTCCGTATCGATCCAAATGATCCGGAGGATGTGgtaagttaatccttcttttcttctatatttaaaaatgcgagggagttggatattacttt-tcatatgctaccattctgcacgtgcctttccaactatggta
















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|113701598|gb|EE679102.1|EE679102
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|60399699|gb|DN232509.1|DN232509
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|32935795|gb|CF040607.1|CF040607
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|86465810|gb|DY232183.1|DY232183
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|71449332|gb|DR830382.1|DR830382
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|37375691|gb|CF624300.1|CF624300
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211238064|gb|FL481625.1|FL481625
EST:     GTAGCTTGCCGGCC-AAMTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|44900308|gb|CK826853.1|CK826853
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|60398835|gb|DN231651.1|DN231651
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|31357633|gb|CD441990.1|CD441990
EST:     GTAGCTTGCCTGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAA-TACATGCTTTCAAATCAGAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|67018352|gb|CO447101.1|CO447101
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|78075367|gb|DV503801.1|DV503801
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211538727|gb|FL481468.1|FL481468
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211477790|gb|FK995982.1|FK995982
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|60348776|gb|DN215749.1|DN215749
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211477791|gb|FK995983.1|FK995983
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|24765200|gb|CA400359.1|CA400359
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211147842|gb|FK968701.1|FK968701
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGWAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|60394898|gb|DN227767.1|DN227767
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|211253693|gb|FL475671.1|FL475671
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
EST: gi|113704163|gb|EE681667.1|EE681667
EST:     GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTT                         AAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT
genomic: GTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaat ... tgtgttgtagAAAGCTGCAAAGCGTAAGAAAATACATGCTTTCAAATCAAAATCCCGCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAATAAAGAGGAAAATTGAACAAGCAGCAACATCTGATTTTCAGGCGCGTAGCTTGCCGGCCAAACTTCGTATCGAACCAAGTGACCCTGAGGATGTTgtaagtgaatctgccctttgttgcaagtcgcaagtaagctaaattttgtggtatcatgtgttcttactgactcttcttctgtgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG