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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag

Basic information

species Zea mays
transcript GRMZM2G030280_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 8
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtttattat-ctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
||| |||||||| ||||| || ||||| ||||||||||||||||| || ||||||||||| |||||||||||||| ||||||||||| ||| |||||||||| | |  | |    |||  ||  |||||   | || | |||          | || | ||        |||    |  | || ||||  ||   || ||  |   |    ||                       
CAAAGCAGATGTCTTTCATGTGTTATCAGGCATGTGGAAGACACCAGCTGAGAGGTGTTTCTTGTGGCTAGGAGGATTCCGACCATCCGAGCTTTTAAAGgtctgtaaagt---cttacgatgttcttgttgtttatttgagccat------ccttctattg-----caaagcccctcctattaccaaa-accaatgtttctaccataatattat---------------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 8
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
 ||||| ||||| || ||  | || ||||| |||||||||||||| || |||||||||||| | ||||| || ||||| ||  |||||||  |  | |||||      |     ||| | | |  | |   | | |||          |||   |||||| | | ||     ||||    |||| ||  | | ||  |||  ||| |    | | ||  |               
TAAGGCTGATGTCTTCCATTTGTTGTCTGGAATGTGGAAGACACCAGCAGAGAGGTGTTTTCTATGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtg-----agctgatttgtgacccttcga--tttgctgt-------tcgcatggtttgttgaaagata----ttgtgacttttctaaaaagtagt--ttttcttggtaacatacagagta---------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 8
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtata-tgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
 ||||| ||||| || ||  |  | ||||| |||||||||||||| || |||||||||||| | ||||| || ||||| ||  |||||||  |  | |||||    ||   |||| || | | |  |  |  | | |||   |  ||| |     |||||| | | |      ||||    |||| ||  |   ||  |||  ||| |    | |                     
TAAGGCTGATGTCTTCCATTTGCTGTCTGGAATGTGGAAGACACCAGCAGAGAGGTGTTTTCTATGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtgagctgatttgtgattgtaacccttcag--tttgctgctct--caagg-----tttgttgaaagaca----ttgtggcttttctaaaaa---gtagttttcttggtaacataca--------------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatg-tgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
 ||||| |||||||| ||  | || ||||| |||||||| ||||| || |||||||||||||||||||| || ||||| ||  |||||||  |  | |||||  | |   || || |  || ||  |  ||||  |  |       ||||   ||| |        |    |    |||| |||  ||    |  | |    |                                 
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgt-caggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgttt--aaatttttttaagaaaa---------------------------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 10
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
 ||||| |||||||| ||  |  | |||||||||||||| ||||| || |||||||||||||||||||| || ||||| ||  |||||||  || | |||||      |   || |  || ||  |   |||  | |||  ||| ||  |   ||||||  ||   | | |     |||  ||  ||    |    |                                      
TAAGGCTGATGTTTTCCATTTGCTGTCTGGCATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttatgctgatccttttcattctagtttca-tggtttag-aaaacgggttttgtagattagtaatggacagttttgtttaaattttttaaaaagaag---------------------------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 5'ss of exon 8
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtttattatctcttgggttctactggagtagcaatgcactttttgttaatacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
 |||   ||||| |||||| |  |||||||||||||||| ||||| || ||||| ||||| |||||||| || || || ||  |||| ||  || |||||||           ||  | | || ||| |  |  || |   | ||| |    || |   ||  |||| ||     |  || |    |  | || || |   |  |                              
TAAGAATGATGTCTTTCACTTGCTATCTGGCATGTGGAAAACACCAGCTGAGAGATGTTTCTTGTGGCTCGGTGGATTTCGTTCATCCGAACTTCTAAAGgtgag--------gtcaaatttcactttgtcttcaccg--attgca-tctgtttctacatagaacataaaaagaatggtcatagggaaaaatg-tgttgaaacag------------------------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 10
CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaatgtgtt-tattatctcttgggttctactggagtagcaatgcactttttgtta-atacatgaagtttgttttctttccaagcactggtgatttcattgttgggttgctgataaaatatgcaactgcag
|||||| |||||||| ||  | ||||| ||||||||||| ||||| || |||||||||||||||||||| || ||||||||  |||||||  |  |||||||||   |  | |    | ||     ||   ||||  ||| |||   |  | ||     | | | | |  | |     ||  | ||||    |     ||||| |                                
CAAGGCTGATGTTTTCCATTTATTATCAGGCATGTGGAAAACACCTGCAGAGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgacccttttaccattttgatggtttccttctgttggggtattcagaccctcaccctgacaaataataggaagacttcatctccatatcc-----atttctt--------------------------------

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|74232818|gb|DT640732.1|DT640732
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|74232819|gb|DT640733.1|DT640733
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
EST: gi|71426016|gb|DR807066.1|DR807066
EST:     GAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAAG                         CT-CTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTC
genomic: GAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAA-Ggtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTC
EST: gi|211365702|gb|FL031151.1|FL031151
EST:     AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAG                         CTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA
genomic: AGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 45

CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 52

CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 48

CAAGGCAGATGTTTTTCACGTCTTATCTGGCATGTGGAAGACACCGGCGGAGAGGTGTTTTTTGTGGCTAGGAGGTTTCCGACCATCTGAGGTTTTAAAGgtatatgcaa ... gcaactgcagCTTCTTTCGACACAACTTGAACCTCTCACCGAACAGCAGCTGTCAGGGATAAGCAACCTTCAGCAATCTTCACAGCAGGCTGAGGATGCTCTTTCACAAG