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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgtagtaatgttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa...

Basic information

species Zea mays
transcript GRMZM5G824831_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 7
--------------GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtac-------agcctcaatgtagtaatgttgtgcact-tgatctagacactgttttgagttgtgacacagtactgctgataatat--tctttcatccgattgtaaataa--------------------------------------------
              |||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||| ||||||||||| ||||||       | |   ||| | ||| |||  | |||| || | |   || | |  | ||   | |    |   || | |  |     ||||   ||| |   |  || |                                            
TATTATTTCTACAGGTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 7
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtac-------agcctcaatgtagtaatgttgtgcact-tgatctagacactgttttgagttgtgacacagtactgctgataatat--tctttcatccgattgtaaataa--------------------------------------------
|||||||||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||||||||||| ||||||||||| ||||||       | |   ||| | ||| |||  | |||| || | |   || | |  | ||   | |    |   || | |  |     ||||   ||| |   |  || |                                            
GTTGATCCCTCAGGATCATACTTCTCCTGGAAAGCATCAGCTATGGGGAAAAATGTCTCCAATGCAAAGACATTTCTTGAAAAAAGgtacatagcataccactaatattgtattgtactacactctgttttcctcaatctgatcagaaataaagtggatttgtttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcag

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaat--gtagtaatgttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || |||||||||||||||||||| ||||||||     |  ||   ||| | |  ||    |   || |    | ||  |  | || |       |  ||   || || | || |   | | |      |  
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcaatagcagttctgcaagcaaaatgtgtggagtgcatcaattttttttgtgtttgtgtccattatgtgctgtgg-ctggtaccccttg-

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgtagtaat-gttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa-
|| ||||| || || ||||| || || ||||| || || || ||||| |||||||| || |||||||||||||||||||| |||||||| ||| |      | || | ||| ||||    |         ||   ||| |    |     |  || || |       ||   | |  | |   | |  
GTGGATCCATCGGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgta-agcttttcatcaatagtagttctgcaagcaaaagcatgtgtgaagtgaatcagaatttgtttttg-tgttgtgtccattatgtgctgtggcccacacc

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgta--cagcctcaatgtagtaatgttg-tgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || ||||||||||| |||||||| ||||||||   ||  |    ||     | ||  ||||  |  |||   |         |     ||  || ||        || | |  |  ||    | ||      
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagatttgtcgtgtcttttttaatgcatctcttcttcccttaccaaaaaaaaaggatgca-tatcttcttcaaaagttgtcaattttgtggtttgg--

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaat--gtagtaatgttgtgcacttgatc-tagacactgttttgagttgtgacacagtactgctgataa-tattctttca-tccgattgtaaataa
|| ||||| ||||| ||||| || || ||||| || || || ||||| |||||||| || |||||||||||||||||||| ||||||||     |  ||  |||  | |  |     |   | | |    | ||  |  |  | ||      |    |   ||| || |  |  | || |  |||      
GTGGATCCATCAGGTTCATATTTTTCTTGGAAAGCTTCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACGTTTCTTGAGAAGAGgtaagcttttcatcagtaacagttcttcaagcaaaaacatgtggagtgcatcaaaatttgttgtgttgtatccattaagtactgatgaaatctgtctgtg-----

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 5'ss of exon 9
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgtagtaatgttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa
|| ||||| || || || || ||||| ||||| || || || |||||||| ||||| || |||||||||||||||||||| |||||||               ||||  | | |  ||  |   ||     || |||  |  ||  ||   |   | ||  || ||||| ||| |           
GTGGATCCATCTGGCTCTTATTTCTCATGGAAAGCTTCTGCAATGGGAAAGAATGTTTCGAATGCAAAGACGTTTCTTGAGAAGAGgtg-------------ataataatttaccatttgtggtgatgagtttatgatcttggaagcatgtcatttcatcttagtctttgatcag-----------

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtac---agcctcaatgtagtaatgttgtgcacttgatctagacactgttttg-agttgtgacacagtactgctgataatattctttcatccg-attgtaaataa
|| ||||| ||||| ||||| ||||| ||||| || || || ||||| || ||||| || ||||||||||| |||||||| ||||||||    |  |  ||| | ||  || ||||   ||  |  | |   | |   | ||  |     |  || ||    | ||| | || || |   | | |   || 
GTGGATCCATCAGGTTCATATTTCTCATGGAAAGCCTCCGCAATGGGGAAGAATGTCTCAAATGCAAAGACATTTCTTGAGAAGAGgtatttaaatcagaatttggt--tgctgtgtcttt--ttaaaatgatatcaagcagcagcctatctttattgtgtttgatacttttgcaacaacaattttttta-

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: PP1S61_202V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgtagtaatgttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa---------------------------------
|| ||||| |||||||| |||||||| |||||||||||||| || || || |||||||||||||| ||||| || || || || ||||    | ||    || |  ||      | |||   |  | |   || |  |||    |   |    | ||| ||  ||     ||   | |  || |                                   
GTGGATCCTTCAGGATCGTACTTCTCATGGAAGGCATCAGCAATAGGCAAGAATGTGTCCAATGCCAAGACTTTCCTAGAGAAAAGgtcagtcatcttcatact--tggcacata-ttgtctttcataactttatccgttacatccatgataagttgacaa-gtttccatatgtaactcgaattggtgacttattcactgggttcttctgttcaagcag

upper sequence: GRMZM5G824831_T03 (Zea mays), 5'ss of exon 9
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgta-gtaatgttgtgcacttgat-ctagacactgttttgagttgtgacacagtac---tgctgataatattctttcatccgattgtaaataa----------------------------------------
|| ||||| ||||||||||||||||| |||||||||||||| || || || |||||||| ||||| ||||| ||  | || || ||||    |||     || ||     | ||   | ||| ||  |  ||    || | |   |  ||| |    |  |||         ||| |   ||  | ||||                                         
GTAGATCCATCAGGATCATACTTCTCATGGAAGGCATCAGCAATTGGCAAGAATGTGTCTAATGCGAAGACTTTCTTAGAGAAAAGgtcggtcctttccatacgttgcactctgttttcgattctgtagtctacgatgtggtagaatgcaggatgagttttgaacgagacgattcgtgtcatatttaatatgagatagtgactcattcgagaggcatactgttacaagcag

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|18181390|gb|BM382600.1|BM382600
EST:     TCAGCCATGGNNNNNNNTGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211269953|gb|FL444406.1|FL444406
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACCGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|148973074|gb|EE024136.2|EE024136
EST:     TCAGCCATGGNNNNNNNTGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|78112696|gb|DV531090.1|DV531090
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCCCCCTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACT
EST: gi|5268558|gb|AI770522.1|AI770522
EST:     TCAGCCATGGTAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAATATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|32830197|gb|CD969875.1|CD969875
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211252215|gb|FK953396.1|FK953396
EST:     TCAGCCATGGGAAAAAATGTGTCCTATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGGAGCTTGATGATGCCATCCACACTGCAATTTTGA
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGG-AGCTTGATGATGCCATCCACACTGCAATTTTGA
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAAAATATGGAGCTTGATGAT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGA-TATGGAGCTTGATGAT
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|32795340|gb|CD947576.1|CD947576
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGGTGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211153309|gb|FL164197.1|FL164197
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctcaatgtagtaatgttgtgcacttgatctagacactgttttgagttgtgacacagtactgctgataatattctttcatccgattgtaaataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG