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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGGGGAGGCTGCCGCGCCTCCTGACCTCGCTTCCGCCTCGCCTCCCCGACCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgctaccgcccctagatcgctggaattttgcgtctctagcagctcgtgcttgtacagttttctgatcgaggcggcactgatgccgtttccccttttggttccag

Basic information

species Zea mays
transcript GRMZM2G157316_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157316_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g16330.1 (Oryza sativa), 5'ss of exon 1
CCGGGGAGGCTGCCGCGCCTCCTGACCTCGCTTCCGCCTCGCCTCCCCGACCGGACCAGCGGCCTCCGTCTGAA--GATGCAGGGCGGCGTCTCCGGATTCCgtaagacgctaccgcccctagatcgctggaattttgcgtctctagcagctcgtgctt-gtacagttt--tctgatcgaggcggcactgatgccgtttccccttttggttccag-----------------
   || || | || | |      |    ||| |||    | |  |   |  || | | |   |   ||   | |  ||||||||||||||| ||||||||||||||| |||  || |||      | ||   |||| ||     | |   |  |   |  |  | ||||  || |  |  | | ||      | |||||     |||| ||                     
-GCGGAAGACCGCGGAGAGGTGGGGGGCCGCGTCCCGACCCCGGCGGTGGTCG-ATCGGTTCCGGACGAGAGGAGCGATGCAGGGCGGCGTGTCCGGATTCCgtaag-cgccgcctccctccccccactcagatttcgccggaatcgagaccggaattccgccccgtttactccgtgcctgaccgcctccccggcgtttgtttgtttgttttttcgctttggttggttgcag
















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|148962075|gb|EE012879.2|EE012879
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|76281436|gb|DV021004.1|DV021004
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|211523741|gb|FL258543.1|FL258543
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|71305646|gb|DR788962.1|DR788962
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|211463964|gb|FL402449.1|FL402449
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|71448463|gb|DR829513.1|DR829513
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|93014294|gb|EB639814.1|EB639814
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|149102614|gb|EE188245.2|EE188245
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|71305918|gb|DR789090.1|DR789090
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|93013209|gb|EB638729.1|EB638729
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|148999432|gb|EE036384.2|EE036384
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|211523736|gb|FL258538.1|FL258538
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|74237515|gb|DT645429.1|DT645429
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGACTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|50336165|gb|CO531291.1|CO531291
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|93013635|gb|EB639155.1|EB639155
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|211523737|gb|FL258539.1|FL258539
EST:     CGGACCAGCGGCCTCCGTCTGAAGAATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CGGACCAGCGGCCTCCGTCTGAAG-ATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|149080963|gb|EE170059.2|EE170059
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|149105307|gb|EE290799.2|EE290799
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|86470247|gb|DY236617.1|DY236617
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCGGGGCGGCGTCTCCGGATTCC                         AAAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|71327756|gb|DR800512.1|DR800512
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|89762002|gb|DY689797.1|DY689797
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
EST: gi|211523740|gb|FL258542.1|FL258542
EST:     CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCC                         AGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG
genomic: CCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgct ... ttggttccagAGAACGCGCCGGTGACGCGGGCGGTCGTCGTCGCGAGCGGCCTCCTGTCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGGGGAGGCTGCCGCGCCTCCTGACCTCGCTTCCGCCTCGCCTCCCCGACCGGACCAGCGGCCTCCGTCTGAAGATGCAGGGCGGCGTCTCCGGATTCCgtaagacgctaccgcccctagatcgctggaattttgcgtctctagcagctcgtgcttgtacagttttctgatcgaggcggcactgatgccgtttccccttttggttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG