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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacatcaaacttgatatcaacag

Basic information

species Zea mays
transcript GRMZM2G010085_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 23
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacat-caaacttgatatcaacag
||||||| | ||||||||||||||||| || ||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||| |||||| | ||||||| |   |||    | |||    ||    ||      || |||| |||   |  ||  || | |         ||    || | |  |  | ||   | |   |||  | |||    
GGCTAGGAGATGTGATACCCTTATCCGTCTAGTTGAGAAAGAGAATCAGGAATATGATGAGCAAGAAAGGCAGGCAAGGAAGGACAAAAGGATGGCTAAGgta---cctctgttcattt--caccttcca------agatctttatttcattgtttgaggctttat--gcactactttgtgtactgttttgtgtagtactttcttcgtttcac---

upper sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 23
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatc-ctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacatcaaacttgatatcaacag
    ||| ||||||| ||||| || |||||||| || || ||||| |||||||||||||||   ||||| |||||  | || ||||| |  ||||| || |  | |  ||   | ||||   |  | |   | ||  ||   || | ||||         |  |  || ||  |  | | ||  | |  || | |                     
----AGGAGGTGTGACACCCTCATTCGACTGGTAGAAAAGGAAAACCAAGAATATGATGAGAGGGAGAGACAAGCTCGCAAAGAGAAGAAACTTGCCAAAGTTAgtttctcgtcatattgtgtgttaa---tagtatagaatttgaatatg--------aatttttctcatact-caagtttaactaatatttcag--------------------

upper sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 23
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacatcaaacttgatatcaacag
    ||| ||||||| |||||  | || ||||| ||||| |||||||||||||||||||||   |||||||||||  | || ||||| |   |||||        || ||   | |      |      | |         || |||     | |   |   || | || |||    |     ||                              
---AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattttaacctaaaatatccgacttaaataacatttatttca--actgttgctttaaccaa-gtttggcgaacaacag-----------------------------

upper sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA07G38050.1 (Glycine max), 5'ss of exon 23
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttg-caatgatctgacatcaaacttgatatcaacag
    ||| ||||||| ||||| || || ||||| ||||| |||||||||||||||||||||   |||||||||||  | || ||||| |  ||||||         |  |   || |    ||  |   | ||  | |   |  |||||||   |    ||   | |  | | |    ||||| | |  | | |                      
---AAGGAGGTGTGACACCCTCATTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAACTTGCTG--------CTAAGgtttgtattttaacctaaaatgc-cggacttaaattatgtttatttcaact--gttgttttaaccaagtttggcgaacaacag----------------------

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|60394449|gb|DN227319.1|DN227319
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|19057932|gb|BM736599.1|BM736599
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGC-CTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|32943371|gb|CF048190.1|CF048190
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|18648750|gb|BM497569.1|BM497569
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|166473608|gb|EG132422.1|EG132422
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAAC
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAAC
EST: gi|5901273|gb|AW042373.1|AW042373
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|60399555|gb|DN232366.1|DN232366
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|67013537|gb|CO442286.1|CO442286
EST:     ATGATGAGCAAGAGAAGGCA-GCAAGGAANGGAGAAA-GGCTNNGCTA-G                         AACATGACTCCA-CAA-GCGAGCTGCACTAA-GAATTCAGAGG
genomic: ATGATGAGCAAGAGA-GGCAAGCAAGGAA-GGAGAAAAGGCTT-GCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGG
EST: gi|60342830|gb|DN209803.1|DN209803
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|87153391|gb|DY398180.1|DY398180
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|22489820|gb|BU049743.1|BU049743
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|166518240|gb|EG073174.1|EG073174
EST:     GATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTC
genomic: GATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTC
EST: gi|78022398|gb|DV490785.1|DV490785
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|7216553|gb|AW562675.1|AW562675
EST:     AATATGATGAGCAAGAGAGGCAAGCA-GGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|19855114|gb|BQ060166.1|BQ060166
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|18648751|gb|BM497570.1|BM497570
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
EST: gi|166687302|gb|EG166934.1|EG166934
EST:     GATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAA
genomic: GATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAA
EST: gi|5915179|gb|AW052820.1|AW052820
EST:     AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAG                         AACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT
genomic: AATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatccta ... atatcaacagAACATGACTCCAACAAAGCGAGCTGCACTAAAGAATTCAGAGGGTGAGAAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacatcaaacttgatatcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA