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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcgtctccacatcctgttccatttcggtttgatcattcatacatgtcatgatgattgacctttttacttgattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 10
gtatttcgtctccacatcctgttccatttcggtttgatcattcatacatgtcatgatgattgacctttttacttgattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG
        | ||  ||| |  || | ||||  | | |   |  || | | ||||||| ||||||| | || | ||||| | |||||||||||||||||||||||||| || |||||| |||| || |||||  ||||||||||||||
-----gtatatcttcatacgattacttttct-tgtaacagtgtatgcttttcatgatcattgaccgtctttcgtgattttctagCTAGGGATTGCTATTGTAAATGACTTTAAGAGTGTTGAGGGAGATAGAGCTCTGGGGCTTCAG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 10
--------gtat-ttcgtctccacatcctgttccatttcggtttgatcattcat-acatgtca-tgatgattgacctttttacttgatta---tgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG
         ||| ||| ||   ||||  ||||  || |   | |||| ||   | | ||   | || | ||| |  || ||  |  || |   || || | || ||||||||||| ||||| ||||| ||| |||||||||||||| |||| |||||||| 
agtatgtaatatattcttcatgacattttgttggatatgaatatgataatatgtcaaataaaaatggttattaatgttgttgttaaatcacattgcaGTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCA-

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 10
-------gtatttcgtctccacatcctgttccatttcggtttgatcat---tcatacatgtcatgatgattgacctttttacttgatta---tgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG
        ||||    |    ||   ||||  || |   | |||| ||    || | | |  ||| | ||| |   | ||  |  || |   || || | || ||||||||||| ||||| ||||| ||| |||||||||||||| |||| |||||||||
gtatgtaatattcta-catggcactttgttggatatgaatatgataatatgccaaataaga-atggttattaatactgttgttgtatcacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCAG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 2
-------gtat-ttcgtctccacatcctgttccatttcggtttgatcat---tcatacatgtcatgatgattgacctttttacttgatta---tgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG
        ||| |||  |    ||   ||||  || |   |  ||| ||    || | | |  ||| | ||| |  || ||  |  || |   || || | || ||||||||||| ||||| ||||| ||| |||||||||||||| |||| |||||||||
gtatgtaatatattctacatggcactttgttggatatgaatacgataatatgccaaataaga-atggttattaatattgttgttgtatcacattgcagTTGGGAATTGCTATTGTCAATGACTTCAAAAGTGTTGAAGGGGATAGGGCTCTAGGGCTTCAG

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|149038823|gb|EE155536.2|EE155536
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATT
EST: gi|32940940|gb|CF045759.1|CF045759
EST:     ACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: ACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|61119511|gb|DN560472.1|DN560472
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATNGTAAATGATTT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTT
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|71763867|gb|DR961804.1|DR961804
EST:     AGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: AGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|149080582|gb|EE169625.2|EE169625
EST:     CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTTCA-GAGTATTGAAGGGGATAGGAC
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTT-CAAGAGTATTGAAGGGGATAGGAC
EST: gi|32940989|gb|CF045808.1|CF045808
EST:     GTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: GTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
EST: gi|148929759|gb|EE285358.2|EE285358
EST:     TTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGG                         CTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT
genomic: CTCTTACACCAGATATCATTGTCTTGACTACTTTGTACAGCATAGCTGGGgtatttcgtc ... gattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtttgatcattcatacatgtcatgatgattgacctttttacttgattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG
                                    tttttacttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcgtctccacatcctgttccatttcggtttgatcattcatacatgtcatgatgattgacctttttacttgattatgtagCTAGGGATTGCTATTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG