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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG

Basic information

species Zea mays
transcript GRMZM2G459642_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459642_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g74310.4 (Oryza sativa), 3'ss of exon 14
gtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
|||||  |    |||||| |||||  ||||| ||||||||  |||| ||||  || | | ||  | | |  |||||||||||||||||| || ||||| |  |||||||||||||||||||| |||||||||||||||||||||
gtatgcctatcacaattgttgattgtttgcttatagttctggtccactttga-ttgataaaaattatatgcacagAGAATGATGACAGAAGAGCCAGATACCTACCAACGGATGCTTCAAAGTCTCATCTCAAAAGCTCAACAG

upper sequence: GRMZM2G459642_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 15
---------------------------gtatgattgaagcaattgctgattca--ttgctgatagttctactccattttgccttaacacaacctgtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
                           | |  |  |  |||| || | || ||  ||| || ||||| |  | ||   || | |           | ||  ||||||||||||||||| ||||| |||| ||| ||||| |||||||| |  ||||| |  | |||||| |||
gcaagaacactattctttcttcccactgcaccaaggttgcaactgtttatccagtttgatgttagtttt--tgcaaactgacctggagtttggcat-tttgcagAGAATGATGACAGAAGAACCTGAGAAATATCAACGAATGCTTCAGAATCTCATTTTTAGAGCTCAGCAG
















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|60346719|gb|DN213692.1|DN213692
EST:     ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG                         AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST: gi|60399844|gb|DN232654.1|DN232654
EST:     ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG                         AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST: gi|60344784|gb|DN211757.1|DN211757
EST:     ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG                         AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST: gi|6056553|gb|AW090943.1|AW090943
EST:     ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG                         AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTNAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST: gi|33091264|gb|CF051258.1|CF051258
EST:     ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG                         AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcattgctgatagttctactccattttgccttaacacaacctgtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
                               ccttaac  putative branch site (score: 3)
                         atttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA