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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaatccgattacttcgcgtagcaagaactctgttcgattgaggacgtcgttttggtgtcaatctgtcaattttgaccgctgatttgctctggtggtgccattttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGGGTGGCACTAGACGAGGTTGGACCGGGGCTGTTCGACGCACTCTTTGCCA

Basic information

species Zea mays
transcript GRMZM2G151863_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g28300.2 (Oryza sativa), 3'ss of exon 2
gtgagaaatccgattacttcgcgtagcaagaactctgttcgattgaggacgtcgttttggtgtcaatctgtcaattttgaccgctgatttgctctggtggtgccattttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGGGTGGCACTAGACGAGGTTGGACCGGGGCTGTTCGACGCACTCTTTGCCA
                                    ||  | ||  |   ||  ||||| ||   |  ||  ||| |       ||||    |  | || ||| | ||   ||||||||||||||||| ||||||||||| ||| ||| |||||| || ||||||||||| || || ||||| || || ||||||||||| || ||||| || |
------------------------------------gtgtgtttttg--tgtttttttg-tgctgaagtgcgaatctg------tgatggttttggatgatgcgaattgt-tagGGGTTCTTGCACGGGCTGAAGAAGGAAGCAGTGGTGGAGGGAGACCATGGGGTGGCCCTCGATGAGGTCGGCCCCGGGCTGTTCGATGCGCTCTTCGCGA

upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 3'ss of exon 2
gtgagaaatccgattacttcgcgtagcaagaactctgttcgattgaggacgt-cgttttggtgtcaatctgtc----aattttgaccgctgatttgctctggtggtgccattttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGGGTGGCACTAGACGAGGTTGGACCGGGGCTGTTCGACGCACTCTTTGCCA
||||| |||| |  |  |||    | |   || ||||    ||| | || ||  ||||| ||||   | |||     | |    | |  ||||    |  | || ||| | ||   ||||||||||||||||| ||||||||||| ||| ||| |||||| || ||||||||||| || || ||||| || || ||||||||||| || ||||| || |
gtgaggaatctggctctttcat-catcgctaaatctg----attaaagatgtgtgtttttgtgtttttttgtgctgaagtgcgaatctgtgatggttttggatgatgcgaattgt-tagGGGTTCTTGCACGGGCTGAAGAAGGAAGCAGTGGTGGAGGGAGACCATGGGGTGGCCCTCGATGAGGTCGGCCCCGGGCTGTTCGATGCGCTCTTCGCGA
















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|211092351|gb|FL156509.1|FL156509
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211097293|gb|FL156532.1|FL156532
EST:     CCAGCGCCGAGGMCGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCTGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211094822|gb|FL156520.1|FL156520
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211094831|gb|FL156529.1|FL156529
EST:     CAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGG
genomic: CAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCC-GGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGG
EST: gi|211087426|gb|FL156471.1|FL156471
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GG-TTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211089875|gb|FL156485.1|FL156485
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGANGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|149008091|gb|EE040331.2|EE040331
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAAGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211092345|gb|FL156503.1|FL156503
EST:     CCAGCGCCGAGGAMGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAARGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211097303|gb|FL156542.1|FL156542
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|116817361|gb|EC860203.1|EC860203
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGACGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211092352|gb|FL156510.1|FL156510
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211094821|gb|FL156519.1|FL156519
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211092342|gb|FL156500.1|FL156500
EST:     CAGCGCCGAGGACGACGCGTCGGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTTGCGGAGGGCGATCATNGG
genomic: CAGCGCCGAGGACGACGCGTCGGGGG-TCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCAT-GG
EST: gi|149055348|gb|EE156262.2|EE156262
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211087431|gb|FL156476.1|FL156476
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211097299|gb|FL156538.1|FL156538
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211092347|gb|FL156505.1|FL156505
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAANGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211087427|gb|FL156472.1|FL156472
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGG
EST: gi|211542042|gb|FL156465.1|FL156465
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAARGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211097302|gb|FL156541.1|FL156541
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGC
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGC
EST: gi|211097294|gb|FL156533.1|FL156533
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211087433|gb|FL156478.1|FL156478
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211089876|gb|FL156486.1|FL156486
EST:     CAGCTCCGAGGACGACGCGTCGGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CAGCGCCGAGGACGACGCGTCGGGGG-TCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211542039|gb|FL156462.1|FL156462
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTNGCGGAGGGCGATCATCGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211094826|gb|FL156524.1|FL156524
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211542045|gb|FL156468.1|FL156468
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAKGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
EST: gi|211094819|gb|FL156517.1|FL156517
EST:     CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGG                         GGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG
genomic: CCAGCGCCGAGGACGACGCGTCGGGGGTCTCTCTGGGCCGCCGCGCCGGGgtgagaaatc ... attttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcaatctgtcaattttgaccgctgatttgctctggtggtgccattttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGGGTGGCACTAGACGAGGTTGGACCGGGGCTGTTCGACGCACTCTTTGCCA
                                           ccattttcct  CT-rich tract
           tcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaatccgattacttcgcgtagcaagaactctgttcgattgaggacgtcgttttggtgtcaatctgtcaattttgaccgctgatttgctctggtggtgccattttcctagGGGTTCTTGCACGGCCTGAAGAAGGATGCACTGGCGGAGGGCGATCATGGGGTGGCACTAGACGAGGTTGGACCGGGGCTGTTCGACGCACTCTTTGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT