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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctgaacatgagttgagtcatgcagaagattgccctaagctttctgcatgatatccttttcatgatagtaataacttgggctctcctcacttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG

Basic information

species Zea mays
transcript GRMZM2G101480_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 2
acctgaacatgagttgagtcatgcagaagattgccctaagctttctgcatgatatccttttcatgatagtaataacttgggctctcctca-cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG
                                               | |   ||  |||  |   |  |   | |    | | | |||| | ||||||||||||||| ||  ||||||||||||||||||| ||||||||||||||||| || |||||| ||||||||||||||||||| |||
-----------------------------------------------cttttcattatttctactgttctctaatcccttgttattctcaacatatgctagatgagcgtgtctcaagtgacctgaagaaaaacctcatgcaagcaagGCTGGACAAGAAGATGACCCAGGCACAGCTTGCACAG

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g27850.1 (Oryza sativa), 3'ss of exon 2
-acctgaacatgagttgagtcatgcagaagattgccctaagctttctgcatgatatccttttcatgatagtaataacttgggctctcctcacttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG
  || ||  | |  |  | |||  |      |||  ||    | ||    | ||    | | |       ||||  ||||   | ||   || ||||||||||||||| ||  ||||||||||||||||||| ||||||||||||||||| || |||||| ||||||||||||||||||| |||
gccccgagaaagcataaattcaatctattacttggacttgcttgtccttttcattatttctactgttctctaatcccttgttat-tctcaacatatgctagATGAGCGTGTCTCAAGTGACCTGAAGAAAAACCTCATGCAAGCAAGGCTGGACAAGAAGATGACCCAGGCACAGCTTGCACAG
















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|211150712|gb|FL424943.1|FL424943
EST:     CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGAC-TGAAGAAAAATCTCATGC
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGC
EST: gi|211199840|gb|FL414699.1|FL414699
EST:     CACATCCCTCAACACCAAGCGCCTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|211134616|gb|FL369498.1|FL369498
EST:     CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|87154044|gb|DY398833.1|DY398833
EST:     CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|14701255|gb|BI233673.1|BI233673
EST:     CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|211297066|gb|FL414882.1|FL414882
EST:     CACATCCCTCAACACCAAGCGCCTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|211171174|gb|FL157590.1|FL157590
EST:     CACATCCCTCAACACCAAGCGCYTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATC
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATC
EST: gi|211426583|gb|FL408876.1|FL408876
EST:     CACATCCCTCAACACCAAGCGCCTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGG
EST: gi|211221428|gb|FL386095.1|FL386095
EST:     CACATCCCTCAACACCAAGCGCCTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|51592547|gb|CV071693.1|CV071693
EST:     CACATCCCCCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTAG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
EST: gi|211508672|gb|FL378338.1|FL378338
EST:     CACATCCCTCAACACCAAGCGCCTCGACGATGACACAGAGAACCTCGCCC                         ATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG
genomic: CACATCCCTCAACACCAAGCGCCTCGACGACGACACAGAGAACCTCGCCCgtgagcaatc ... cttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgatatccttttcatgatagtaataacttgggctctcctcacttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG
                                    ctctcctcacttat  CT-rich tract
                    atagtaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctgaacatgagttgagtcatgcagaagattgccctaagctttctgcatgatatccttttcatgatagtaataacttgggctctcctcacttatgctagATGAGCGAGTTCCAAGTGACCTGAAGAAAAATCTCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT