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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG

Basic information

species Zea mays
transcript GRMZM2G042074_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 22
gtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatag-catctaaa------taacctattttc-cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG----------------
||| ||    | |  |  |    || ||  |     |||  || | |||||| | | ||||| ||      |   | |||  | |||||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| |||                
gtatttt---actaaatga-ttgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAGGTAAGTAAATTGTAAT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 22
gtacttatcaattggacaagcctctgttttttggcagttgagtatctgcattatag-catctaaataac------ctattttc-cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
||| ||    | |  |  |    || ||  |     |||  || | |||||| | | ||||| ||  |       | |||  | |||||| ||||||||||||| || || ||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||| |||
gtatttt---actaaatga-ttgctattagtccatggttttgtttttgcattttgggcatctgaaacattgtgtaccattaccacagTGGTTTGGTGAAGGAGAGAAGTTTGTGAAAGCTGTATTTTCACTGGCAAGCAAAATTGCTCCAAGTGTTATTTTCGTGGATGAG

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 5
---gtactta-tcaattggacaagcctctgttttttggcagttgagtatctg--cattatagc-atctaaataacctatttt---ccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
     | ||  |  | |||       |   | | |  ||  |    ||  ||  |||| || |  | |   |  || |||||    |||||| ||||||| || ||||| |  || |||||||||||||| ||||| |||||||||||||| || || || ||||| ||||| 
gttaaatttgcttcactgggtttattttaatgtctctgctatcagttagttgttcattttatctgtgttcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAGTATGTCAAAGCTGTTTTTTCCCTGGCTAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
gtacttatcaattggacaagcctctgttttttg-gcagttgagtatctgc----attatagcatctaaataacctattttc---cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
|||   ||  |||| | |   || | ||| ||| | | ||   | | |||     ||| |  |   | ||    |  |||    |||||| ||||||||||||| ||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| ||||||
gtatcaat--attgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 18
---gtacttatcaattggacaagcctctgttt-tttggcagttgagtatctgcatta----tagcatctaaataacctattt--tccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
    || ||   ||||  |  ||  |   | |  || | | ||   |   | ||| |     || ||  | ||    | |||  | |||||| ||||||||||||||||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| || |||
gtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
gtacttatcaattggacaagcctctgttttttg----gcagttgagtatctgcatta-tagcatctaaataac----ctattt--tccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
     ||| |||     |||   || |||||||    | | ||   | | ||| | | |  ||   |||  |      | |||  | |||||| ||||||||||||| || |  || |||||||| ||||| || || || ||||||||||||||||| |||||||| ||||||
----gtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
-----gtacttatcaattggacaa-------gcctctgttttttggcagttgagtatctgcattatagcatctaaataacctattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
      ||    ||| | ||   |       | ||||||| |  |  |||||   || |  | |  |   | |    |   |  ||  |||||| ||||||| || ||||||| |||||||||||||||||| |||||||||||||||||||| || || || ||||| ||||| 
gttagatatgcttcactgggtttattttaatgtctctgttatcagttagttgttcattttaactgcattcttttcccattttgctt--cagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 18
---gtacttatcaattggacaagcctctgttt-tttggcagttgagtatc-tgcattatagcatctaaataacctattttc----cagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
    || ||   ||||  |   |  |   | |  |  | | ||   | || | ||||| ||   |   |||   | ||||     |||||| ||||||||||||||||||  || ||||| || ||||| ||||| || ||||||||||||||||| |||||||| || |||
gtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcatta-agtgacaggatattgtttttttgttgcagTGGTTTGGTGAAGGAGAAAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGATGAG

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|67017525|gb|CO446274.1|CO446274
EST:     AGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAG                         TGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGT
genomic: AGGCTGGTGCTAATTTCATAAACATATCGATGTCAAGCATCTCTTCAAAGgtacttatca ... tattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttttggcagttgagtatctgcattatagcatctaaataacctattttccagTGGCTTGGTGAAGGAGAAAAATTCGTGAAAGCTGTTTTTTCACTGGCAAGTAAAATTGCTCCAAGTGTAATTTTTGTGGACGAG
                                     aaataac  putative branch site (score: 2)
                                           cctattttcc  CT-rich tract
                                    taaataacctatttt  TA-rich tract