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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaatagggggtggacatattgtggtgtggaggtccaggttctgtaatttcgtagtcttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAGTAAATCTCCAGG

Basic information

species Zea mays
transcript GRMZM2G152552_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 3
gtgagtaaatagggggtggacatattgtggtgtggaggtccaggttctgtaatttcgtagtcttatgaattacaactactg-tatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAGTAAATCTCCAGG---
|| |||| |||  |  | || ||  ||  |||   |  | || | ||||||   | || ||||||| |  | |||||     | ||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||    |||||||| | ||||      
gtcagtacataatgc-tagatattctgatgtgaaaactttcaagatctgta---ttgtggtcttattagctgcaactgtaactctgcagGATCATCCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAGAAAACCAAGGACAAGAC---CGCAAAGTAGAGCTCCTTTGTA

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G41280.1 (Glycine max), 3'ss of exon 3
gtgagtaaatagggggtggacatat-tgtggtgtgga-ggtccaggttctgtaatttcgtag----tcttatgaattacaactactg--tatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAG---TAAATCTCCAGG
||  ||   |             || |   || ||     |     || || || ||  | |     |||    | |       |||  | || ||||||||||| ||||||||||| || ||||| |||||||| || |||||  |||| || ||||| || ||||| |||  ||||   |||   | | | |     
gtttgtttttctcaatcttcttaatctacagtatgtttaattttctttgtgcaaattgatggagtaccttgcttacttttgtctctggttctgtagAATCATTCGAGCTTTCTTGGTTGAAGAGCAAAAGATTGTGAAAAAGGTATTGAAGATCCAAAAGACAAAGGAAAAGCAAGCTTTGAAGGGCTGAGTTTTG---

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G14980.1 (Glycine max), 3'ss of exon 3
-gtgagtaaatagggggtggacatattgtggtgtgga-ggtccaggttctgtaatttcgtag----tcttatgaattacaactactg--tatgc-agAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAG---TAAATCTCCAGG
 ||  ||   |      |   | || | |  | ||     |     || || || || || |     |||    | |       |||  | ||  ||||||||||| ||||||||||| || ||||| |||||||| || |||||| |||| || ||||| || ||||| ||   ||||   |||   | | | |     
ggtttgtttttctcaatttt-cttagtctactatgcttaattttcattgtgcaaattagtggagtaccttgcttacttttgtctctggttctgttaGAATCATTCGAGCTTTCTTGGTTGAAGAGCAAAAGATTGTGAAAAAGGTCTTGAAGATCCAAAAGACAAAGGAAAAACAAGCTTTGAAGGGCTGAGTTTT----

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G69620.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtaaatagggggtggacatattgtggtgtggaggtccaggttctgtaatttcgtagtcttatgaattacaactactgtatg---cagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAGTAAATCTCCAGG---
         | |    ||     | | | || |     |   |  | |||||      |    | | |||      |  ||| ||   ||||||||||||||| ||| | || |||||||| |||||||| ||||||||  ||||  | || ||  | ||||| |||   ||| | |||| |   || ||    
-------gttcgttcttgagttcaattttgtatttgctttgtgcctttgtaaccaaagacaaatcttaatggttgttcttgtgtgttacagAATCATTCGTGCCTTCCTTGTGGAGGAGCAAAAGATTGTGAAGAAGGTTTTGAAGCTTCAGAAGGCAAAGGAAAAGGTTGCTCCCAAGTGA---TCTAGACCC

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S57_72V6.1 (Physcomitrella patens), 3'ss of exon 3
------gtgagtaaatagg--gggtggacatattgtggtgtggaggtc--caggttctgtaatttcgtagtc--ttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAG--TAAATCTCCAGG
      ||  | |    ||    || | |        ||  | | |||  ||   | |||| |    |  |    || | |||  |  |     | |||| || ||||| |||||  |||||||||||||||| ||||| ||||||||||| || || || || |  ||||| ||    ||||| |||  | || ||  |  
aaaatcgttggaagtctggctaagtcgtctctggccagtaggtacgtcggcataatttgtagtgatatgtttggctaaggatttaagttgtatgacgcagCATTATTCGGGCTTTTCTGGTCGAGGAGCAGAAAATTGTAAAGAAGGTCCTCAAGATCCAGAAGAGTAAGGAGAAATTGGCTGCCAAGGCTCAAACTTAA--

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S39_344V6.1 (Physcomitrella patens), 3'ss of exon 3
--------gtgagtaaatagggggtggacatattgtggtgtggaggtccaggttctg------taatttcgtagtcttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGC--AAAGTAAATCTCCAGG
         ||  | | |      |     |  ||| |||| |   | | ||   ||      | || |  |    || ||||   ||| ||   | ||||| |||||||| |||||| | |||||||||||||||||||| ||||| || ||||| || || ||  | ||||| ||    |||||  ||| | | |||  |  
attagtcattgtctgatttctttttaacagttctgttgtgttggccttctgggcatgcttggatcatgttttgcatttctgaac--caagtaaattttgcagCATCATTCGCGCTTTCCTTGTCGAGGAGCAGAAGATTGTGAAGAAAGTACTGAAGATCCAGAAGTCAAAGGAGAAATTGGCTGCTAAAACTCAGTCTTAA--

upper sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S2_268V6.1 (Physcomitrella patens), 3'ss of exon 3
------gtgagtaaatagg--gggtggacatattgtggtgtggaggtccaggtt--ctgtaatttcgtagtc--ttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAG--TAAATCTCCAGG
      || || |   |||    || | |        ||  | | |||    ||   |||| |    |  |    || | |||  |  |     | |||| || || || |||||  |||||||||||||||| ||||| ||||||||||| || || || || |  ||||| ||    ||||| |||  | |||||  |  
aaaatcgttagaagtcaggctaagtcgtcgctggccagtaggtacgtcggcattatttgtagtgatatgtttggctaaggatttaagttgtgtgacgcagCATTATCCGGGCTTTTCTGGTCGAGGAGCAGAAAATTGTAAAGAAGGTCCTCAAGATCCAGAAGAGTAAGGAGAAATTGGCTGCCAAGGCTCAATCTTAA--

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|28986376|gb|CB351105.1|CB351105
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32939085|gb|CF043904.1|CF043904
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|50337739|gb|CO532865.1|CO532865
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTTTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|33094263|gb|CF054257.1|CF054257
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|33094473|gb|CF054467.1|CF054467
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32945005|gb|CF049824.1|CF049824
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGGAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32940137|gb|CF044956.1|CF044956
EST:     GTGGACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|15056983|gb|BI360955.1|BI360955
EST:     ACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: ACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|17930541|gb|BM267501.1|BM267501
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|18174677|gb|BM350065.1|BM350065
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|33094622|gb|CF054616.1|CF054616
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTCCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|18163314|gb|BM333153.1|BM333153
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|18163956|gb|BM333795.1|BM333795
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32805280|gb|CD957516.1|CD957516
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|166639382|gb|EG309286.1|EG309286
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCCTTCTTGGTCGAGGAGCAAGAAGATTGTCAAGAAGGTCC
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCA-GAAGATTGTCAAGAAGGTCC
EST: gi|32940891|gb|CF045710.1|CF045710
EST:     ACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: ACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32939901|gb|CF044720.1|CF044720
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|32848628|gb|CD988309.1|CD988309
EST:     ACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTTTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: ACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
EST: gi|78104834|gb|DV523252.1|DV523252
EST:     GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAG                         AATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT
genomic: GTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTGTTAGGGAGAGgtgagtaaat ... ctgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggtccaggttctgtaatttcgtagtcttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAGTAAATCTCCAGG
                             ttatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaatagggggtggacatattgtggtgtggaggtccaggttctgtaatttcgtagtcttatgaattacaactactgtatgcagAATCATTCGTGCTTTCTTGGTCGAGGAGCAGAAGATTGTCAAGAAGGTCCTGAAAATACAAAAAACCAAGGACAAGACAGCTGCAAAGTAAATCTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG