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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag

Basic information

species Zea mays
transcript GRMZM2G059671_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 5'ss of exon 14
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
 ||||| |||||||||||||||||||| |||||||| ||||| ||| |||||||||| ||||||||||| || |||||||||| ||| ||||||||||||||||| ||||| || ||| | |||||||          ||  ||||| | |||  ||   ||   || ||  |||  ||  |  | |    ||   |                             
TGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGCAACAACCATGGAGTACTTTGAATCCAGCTCAGgtttgtatctcctgttttcttcatcaca--------cggatattttccaacttcggacgaactgaattgaacaaagtct--acctgttcacttgcag-----------------------------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G37570.2 (Glycine max), 5'ss of exon 14
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
|||||| || ||||||||||| |||||||||||||| ||||| ||||| |||||| |    |||||||| ||||| ||||||||||| |||||| | ||||||||      |   || ||  ||  |||| |               ||   |||||| | ||      | |  ||  |  | | || |  ||||| | ||| | |   ||  || | |       
CGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGATCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCACCACAGgtttgttgtataactttgatatatttcagtgtg------------cttatgcttagattttcc-----aatacgattat--attgctttgatttttatgaaagattctttaagatctga-------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G34890.1 (Glycine max), 5'ss of exon 14
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
 ||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||||||    |||||||| ||||| ||||||||||| |||||  | |||||||| ||   |   || ||  ||  |||| |     ||    | | |  | |||    ||     |   ||   |  | ||  |||      |  |    ||                       
TGAGCCATCCAATGAGAAGTCAGATGTTTACAGCTTTGGTGTCATCTTGTGGGAGCTCGCAACATTGCAACAGCCTTGGAGTAATTTGAATCCGCCACAGgtttgtat---aactttgatatatttcagtgtgcttatgcttatattttccattacgactatattgttctgatttttatgaaagtcttaggcatgagcaggaa-----------------------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G07610.1 (Glycine max), 5'ss of exon 15
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
 ||||| || |||||||||||||||||||||||||| |||||||||||||||||||||   |||||||| |||||||||| ||||||||||||||| ||||||||      |    | || ||| |   |||  || | | ||||    |||| | |  |     ||    |  ||  |||  || | ||    ||  | |||  |  |                 
TGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGATTAATTTAAATCCAGCACAGgtttgttgtatagctgtgatacatga---tattgcagt-atgtttat--gcttaatagttgtattatt---attattattatattttttcagcatttatgaaacttgtg-----------------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G21480.1 (Glycine max), 5'ss of exon 13
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcaca--gtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
 ||||| || ||||||||||| |||||||||||||| |||||||||||||||||||||   |||||||| |||||||||  ||||||||||||||| ||||||||      |    | || ||| | |  |||  |  || | | ||  ||| | ||    ||    ||    |  ||  |||  |  | |   | || |||                          
TGAGCCATCGAATGAGAAGTCCGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGCAACAGCCATGGGTTAATTTAAATCCAGCACAGgtttgttgtatagctgtgatacatgatattgtagtatgtttatgcttaatagttctattattatt--attattattattgttat-tgttgttgctgttattat-------------------------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 5'ss of exon 13
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagc-tttagatataccccatggagaaaatccttaagttctctcttttttgtta-aaaaatacgtacaattttacttgcag
 ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||||   |||||||| || |||||| |||| |||||||| ||||||||    |  |    || ||  |||| ||  || | | |||  || | | || ||| ||  | || ||      |  || | |  | || | | |  |  || ||||| | || | ||           
TGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGCAACAACCATGGGGTAACTTAAATCCGGCTCAGgt----actttccactctaaacatctcaa-ataataatgatattattttgcatttggaagtccctcactctacatttcataacatgctatatatgatcatacaaaaaaatgttccatag---------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 13
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacg-tacaattttacttgcag
 ||| | |||||||| ||||| ||  | || ||||| ||| ||||||| ||||| |||   |||||||| || || |||||||||||||||||||| ||||||||    ||     ||||| |   ||       | |||  |  |  |     |||        |  |||| | |  | | | |     |||| | | ||   | | | | ||||| |        
TGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGCAACAACCTTGGAGTAATTTAAATCCAGCACAGgtttgt-cttctgaagttatgtaatgca-------agtgaaatcattgaa----aga--------agagagagattgttgatgattatatttttctttgaagggagatgatgcaattctt-------

upper sequence: GRMZM2G059671_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 5'ss of exon 13
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag
 ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||| |||| |||||   ||| ||||   |||||||||||||||||||  |  | ||||    | |||| ||   ||| |  |||    |    |  ||| || | |   ||  |||||  |  ||    | |    ||  | ||    |  |                   
TGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGCAAAGGCCTTGGAAACATTTAAATCCAGCTCAGgta-gtttgtcattacct-tgcagcaagctataa--ttgttagtaaaaatatttgga-agatatca--gagaacttgtttgtaatattaagttgctatttggtacaa-------------------

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|20802940|gb|BQ293990.1|BQ293990
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGT
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGT
EST: gi|19770366|gb|BQ035087.1|BQ035087
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19822326|gb|BQ048350.1|BQ048350
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|76284240|gb|DV023808.1|DV023808
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|26456039|gb|CA827622.1|CA827622
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|67042437|gb|CO468692.1|CO468692
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|149096725|gb|EE182499.2|EE182499
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|113703759|gb|EE681263.1|EE681263
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|88757722|gb|DY541863.1|DY541863
EST:     GGGAGCTTATGACATTGCAGCACCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78110653|gb|DV529058.1|DV529058
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60358265|gb|DN225238.1|DN225238
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60357002|gb|DN223975.1|DN223975
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|148945985|gb|EC891279.2|EC891279
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|211160526|gb|FL223272.1|FL223272
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19770367|gb|BQ035088.1|BQ035088
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78544160|gb|DV621658.1|DV621658
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|19770019|gb|BQ034740.1|BQ034740
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGGCAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
EST: gi|78544345|gb|DV621843.1|DV621843
EST:     GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAG                         GTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC
genomic: GGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatct ... ttacttgcagGTCGTTGCAGCGGTTGGTTTCAAGGGACAAAGGCTTGAGATCCCAAGCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGCAGCAGCCATGGAGTAATTTAAATCCAGCTCAGgtttgcatctcatgctttatgcatcacagtatcacattgacgttttctagctttagatataccccatggagaaaatccttaagttctctcttttttgttaaaaaatacgtacaattttacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA