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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG

Basic information

species Zea mays
transcript GRMZM2G094051_T06
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 3
gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
       | ||   | ||| ||  ||      | |   ||  ||||| ||| || ||  |      |  || |      |  ||||| || ||||||||||| ||||||||||||||||||||||||||||| |||||||||
------gtgagaaac-tataccgctacggcttaaaat-tgtctttgtttgcataagcattgacagttcgctatgctttatgtagTATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAG

upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 2
------------gtgagtctcaggttcata-tgccagtattttacagaggatgaat---ttgtatgcttatgctg-ttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
             | |||   |   | ||| || || |   | | ||| |||||     ||||||| | |||||  | || ||  ||||||||  ||  ||||| || ||||||||||| |||||||||||||| ||||||||  |||| |||||||||
gtaaggaaccacttaagttgtattgttataatgtcactgact-atagatgatgatctggttgtatgttgatgctaatgttacaaatctgttga--ctgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG

upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgc-----tgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
         | || ||| | | |   | || ||    || |  |||| ||| | ||      ||||    ||   | |  |   |  || || || || |||||||| |||||||||||||| ||||||||||| |||||||| |||
-------gtatgt-catttacaatgttctttcaataaattagcttgt-tgcgtgtgaaggagtgttgattataattatgaatcttttagGATCAATGCTATGCACCCGAAGACCAGGAAGATTTTGCAGCTTCTACGATTGAGACAG

upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20182 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
                  ||    |  |||   ||   | | | ||||         | || ||  ||  | |      | |||||| |||| |||||| || |||||| ||||||||||||||||||| ||  || | |||
-------------gtgagtggtttttctttctcgattttaagtctgtacaaacggagtattatcttttgttttca----tccagTATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAG

upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 3
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
                |  |  | | ||       |  |  |  |   | |  | |  || |    ||| | || |   | |||||| |||| |||||| || |||||| ||||||||||||||||||| ||  || | |||
---------------gtgggtgaattttccttctcgattttaagtccgtacaaacggagtataaattttgttttca---tccagTATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAG

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|211364904|gb|FL335329.1|FL335329
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211439886|gb|FL309186.1|FL309186
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGAC-AGGAAGA
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGA
EST: gi|211381235|gb|FL355200.1|FL355200
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAA
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAA
EST: gi|211197410|gb|FL309893.1|FL309893
EST:     TCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGAT
genomic: TCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCC-GGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGAT
EST: gi|211467480|gb|FL327940.1|FL327940
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211099200|gb|FL356880.1|FL356880
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCT
EST: gi|211430944|gb|FL367566.1|FL367566
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211331288|gb|FL346026.1|FL346026
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|76281808|gb|DV021376.1|DV021376
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211467080|gb|FL315617.1|FL315617
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211425293|gb|FL350052.1|FL350052
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211419805|gb|FL340213.1|FL340213
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211489662|gb|FL352063.1|FL352063
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|31558661|gb|CD527873.1|CD527873
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211262500|gb|FL327821.1|FL327821
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211430817|gb|FL361882.1|FL361882
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211489013|gb|FL325724.1|FL325724
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
EST: gi|211427800|gb|FL348316.1|FL348316
EST:     TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGG                         TATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT
genomic: TTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagtctca ... gaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG
           aatttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctcaggttcatatgccagtattttacagaggatgaatttgtatgcttatgctgttttccatttctgttgaaactacagTATTAACGCCATGCACCCTAAGACCAGGAAGATCTTGCAGCTTCTGCGATTGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT