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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa...

Basic information

species Zea mays
transcript GRMZM2G112865_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 5'ss of exon 3
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgt---aattggaacgca------agtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa
||||||||||| ||||| ||||||||||||||||||||||| ||||| |||||   || ||  ||         | ||||||| ||| |   || ||  ||| ||||| |     |  ||| |||  |||| |||| ||||| || ||  ||        
GCGAAGGAGGTGCGGCGCAAGGCGGATCAGATGGTGCAGCTCGGGAAAGAGgtaaaaactgctacctgtgaaacattctcctgttgccatagaactat-aacctgaaaaaaattactgtttagtgccatccatgaacctatgtagagctttg--------

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 3
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggc-actgactgtaaa-
||||||||||| |||  ||| |||||||||||||||||||| || || ||||||        |      |    |  | |  |  | |    | |    | | |  |  ||     | || ||  |  || ||| ||||    | | |||   
GCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAGgtatacattctgtcgagatgaaaactcaagctggaaattctcgttct-tgtgcaactcttgttctgaattctc-atcctttgctgggccgtaggcggtagca
















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|37393499|gb|CF634015.1|CF634015
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60353121|gb|DN220094.1|DN220094
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|22490485|gb|BU050408.1|BU050408
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|21987795|gb|BQ779323.1|BQ779323
EST:     GGAT-AGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGG-GATGAT
genomic: GGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60397912|gb|DN230728.1|DN230728
EST:     GGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: GGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|87151864|gb|DY396653.1|DY396653
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|21987566|gb|BQ779094.1|BQ779094
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGCGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|18965108|gb|BM661397.1|BM661397
EST:     GGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: GGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|19058032|gb|BM736699.1|BM736699
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|32909297|gb|CF014109.1|CF014109
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|22545985|gb|BU098344.1|BU098344
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa

-  AAGGAG
- - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - -  AAGGAG