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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatgatgatatgtcagctacgcaatttggattcctgctagtgcttcgacgaagtgactgacggtgttttccgtgttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGGGCGCCGCTGTCCGGGAAGGCCGTCGCGGCGCTGTGCGTGACGAGCTTCG

Basic information

species Zea mays
transcript GRMZM2G119265_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119265_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g65590.1 (Oryza sativa), 3'ss of exon 1
gtgtgtatgatgatatgtcagctacgcaatttgg-attcctgctagtgcttcgacgaagtgactgacgg--------------tgttttccgtgttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGGGCGCCGCTGTCCGGGAAGGCCGTCGCGGCGCTGTGCGTGACGAGCTTCG
|| |||    |    |||||  |    || |||   |   |  |  |  || |  ||| |  |  | ||              ||  || | ||| |   | | |   | |||||||||||||||||| ||||||||||||| | ||   |||| |||||||| | || |||||||| || |||||||||||| |||      
gtttgtgatttatcctgtcaattggttaagttgttgtgtttagttatttttgggtgaaataccgtatggatcagtggctaaagtgaatttcttgtagACACTGTCGACGTCGGAGCGGCAGCCGCAGCCGGAGAAGAAGCCGCCACGGACGAGGCCGCCGCTGCCAGGCAAGGCCGTGGCCGCGCTGTGCGTGGCGA------
















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|211223642|gb|FL051772.1|FL051772
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225710|gb|FL051790.1|FL051790
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCASCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223637|gb|FL051767.1|FL051767
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|101397267|gb|EB820557.1|EB820557
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225697|gb|FL051777.1|FL051777
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATT                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGAYGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225709|gb|FL051789.1|FL051789
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211221584|gb|FL051760.1|FL051760
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225698|gb|FL051778.1|FL051778
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211227757|gb|FL051793.1|FL051793
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-SCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225704|gb|FL051784.1|FL051784
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCASCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225703|gb|FL051783.1|FL051783
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCKGCTGCGCGCACTGATG                         GCACTGACGGAACGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225708|gb|FL051788.1|FL051788
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|149112056|gb|EE191226.2|EE191226
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211221585|gb|FL051761.1|FL051761
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223632|gb|FL051762.1|FL051762
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223639|gb|FL051769.1|FL051769
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-SCGCAGCTGGAGAAGAAGCCGACGCGCGGGAKG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225700|gb|FL051780.1|FL051780
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223644|gb|FL051774.1|FL051774
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211221583|gb|FL051759.1|FL051759
EST:     AAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211227756|gb|FL051792.1|FL051792
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225699|gb|FL051779.1|FL051779
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-SCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223646|gb|FL051776.1|FL051776
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCASCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225707|gb|FL051787.1|FL051787
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211225711|gb|FL051791.1|FL051791
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211221582|gb|FL051758.1|FL051758
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223634|gb|FL051764.1|FL051764
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223645|gb|FL051775.1|FL051775
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCA-CCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
EST: gi|211223638|gb|FL051768.1|FL051768
EST:     GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATG                         GCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG
genomic: GAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 2

TTCGTCGAAGCACCCTAGTCGTCGTAGCGGCCTACGGGCTCTTGGGCAGAGAGAGAAGCTGCATAGCCTGCATATGCTCCAGCTGCTGCGCGCAATGATGgtgtgtatga ... gttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGGGCGCCGCTGTCCGGGAAGGCCGTCGCGGCGCTGTGCGTGACGAGCTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcctgctagtgcttcgacgaagtgactgacggtgttttccgtgttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGGGCGCCGCTGTCCGGGAAGGCCGTCGCGGCGCTGTGCGTGACGAGCTTCG
                          gactgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtatgatgatatgtcagctacgcaatttggattcctgctagtgcttcgacgaagtgactgacggtgttttccgtgttggtgcagGCACTGACGGAGCGGCAGCCGCAGCTGGAGAAGAAGCCGACGCGCGGGAGGGCGCCGCTGTCCGGGAAGGCCGTCGCGGCGCTGTGCGTGACGAGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT