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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAATGAGAAGCTAGGTAAATCTGATGATGTTCTGTCAGCTGCAGAGAGATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgttctgaaccgattattttttttctttttgaactgagggacaccccatttccattatgacatagtggaaatacagcagtttgaaagtataaa...

Basic information

species Zea mays
transcript GRMZM2G047860_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047860_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 4
AAGAAATGAGAAGCTAGGTAAATCTGATGATGTTCTGTCAGCTGCAGAGAGATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgttctgaaccgattattttttttctttttgaactgagggacaccccatttccattatgacatagtggaaatacagcagtttgaaa-gtataaa-
|||||| || || ||  ||||| |||||||||| || |||||||| ||||||||||||||||| || |||||||||||||||||||| ||||||||||||||| ||||||||  |||  |     |     || || |     |  |  || | | |      |||     |    | | || |  |   ||  || | |  
AAGAAAAGAAAACCTGAGTAAACCTGATGATGTGCTATCAGCTGCGGAGAGATATATTGAACAGAATGGACCAGAAGCATTTGAGAAACTCATCAGCAAGgtattcttgttcaaaactaaaatcatcacaactattaggg--aaatgcaactctagtatatggatgttcatgctttattccatccctccaaagtgtttgagg
















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|40337486|gb|CK371556.1|CK371556
EST:     TATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|60342892|gb|DN209865.1|DN209865
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|37400289|gb|CF637495.1|CF637495
EST:     TATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|33094100|gb|CF054094.1|CF054094
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|32917049|gb|CF021861.1|CF021861
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAGGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|211053628|gb|FL481081.1|FL481081
EST:     ATATA-TGAACAAAACGGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCARGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: ATATATTGAACAAAAC-GGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|33103180|gb|CF063140.1|CF063140
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|32933985|gb|CF038797.1|CF038797
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAGAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|33104168|gb|CF064128.1|CF064128
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|47961761|gb|CN844470.1|CN844470
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACA
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACA
EST: gi|32933645|gb|CF038457.1|CF038457
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|94472096|gb|EB701054.1|EB701054
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|116828198|gb|EC855483.1|EC855483
EST:     GATATATTGAACAAAACGGA-CAGAAGCATTTGAGAAGCTCATCAGCAAG                         TC-NCGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|76014693|gb|DT941863.1|DT941863
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|86465815|gb|DY232188.1|DY232188
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
EST: gi|24767007|gb|CA402152.1|CA402152
EST:     GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAG                         TCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT
genomic: GATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgt ... ttaattgcagTCTACGAAGTCTTCGAAGTCAAGGAACACAAAGCGGTTGAACTTGGAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAATGAGAAGCTAGGTAAATCTGATGATGTTCTGTCAGCTGCAGAGAGATATATTGAACAAAACGGACCAGAAGCATTTGAGAAGCTCATCAGCAAGgtactcttgttctgaaccgattattttttttctttttgaactgagggacaccccatttccattatgacatagtggaaatacagcagtttgaaagtataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataca