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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcctcacgtgcctgggggggtgcttcgggggggggggggggattcggttgtgaaaggttcttccttcgggcgaaatatctgctctggatgcca...

Basic information

species Zea mays
transcript GRMZM2G001265_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001265_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 1
--ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatc--ctcacgtgcctgggggggtgcttcgggggg--gggggggggattcggttgtgaaaggttcttccttcgggcgaaatatctgctctggatgcca
  ||||||| |||||  | | ||||||||||||| || || ||| || ||||||| || ||| |||  |||||||| ||||||||||  |||||||||||||||   |||   |||     | |  ||||| |    |||||   ||| |    |  |||| |  || | ||      | |||   ||| ||     | || |   
CTACTACGCGGTCGTGGTGTACAACTACGGCCCC-GCGCTCTTCGCC-GGCGGCGCCAGCACCCTCCTCGCGCTCGTCGTCCTGCTCCTCTTCCACTTCCTGgtaactattggctcgaactcttaaggggggggggggggggtttgggtgtcaaaaacggt-gaaaacgattagctggttgggtcgaatctcgcaagtagacg---
















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|93016010|gb|EB641530.1|EB641530
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211173364|gb|FL201332.1|FL201332
EST:     GAGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CGTTGCTATGC
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagC-TTGCTATGC
EST: gi|92088036|gb|EB484267.1|EB484267
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGAACCCTGG
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGA-CCCTGG
EST: gi|211473726|gb|FL264990.1|FL264990
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGGACCCTGG
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGG-ACCCTGG
EST: gi|211476241|gb|FL265001.1|FL265001
EST:     GCGGCACCGCTCTCGCTGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211471206|gb|FL264985.1|FL264985
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476252|gb|FL265012.1|FL265012
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476253|gb|FL265013.1|FL265013
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473736|gb|FL265000.1|FL265000
EST:     GCGGCACCACTCTCGCCGCGCTCGC-GTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473733|gb|FL264997.1|FL264997
EST:     CGGCACCACTTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCCTGTTCACGGACCCTGGT
genomic: CGGCACCACT-CTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473732|gb|FL264996.1|FL264996
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476242|gb|FL265002.1|FL265002
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476244|gb|FL265004.1|FL265004
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476243|gb|FL265003.1|FL265003
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTT
EST: gi|211473722|gb|FL264986.1|FL264986
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|93012311|gb|EB637831.1|EB637831
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|67012486|gb|CO441235.1|CO441235
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476250|gb|FL265010.1|FL265010
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473730|gb|FL264994.1|FL264994
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473723|gb|FL264987.1|FL264987
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTYTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|76919123|gb|DV167601.1|DV167601
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473735|gb|FL264999.1|FL264999
EST:     GCGGNACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGNTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473731|gb|FL264995.1|FL264995
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473729|gb|FL264993.1|FL264993
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|71298289|gb|DR785121.1|DR785121
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473734|gb|FL264998.1|FL264998
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476251|gb|FL265011.1|FL265011
EST:     GCGGCACCACTCTCGCCGCGCTCGC-GTCCTKCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTC
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTC
EST: gi|211476247|gb|FL265007.1|FL265007
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211473724|gb|FL264988.1|FL264988
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211173367|gb|FL201335.1|FL201335
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
EST: gi|211476245|gb|FL265005.1|FL265005
EST:     GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTG                         CTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT
genomic: GCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGT

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: 47 (upstream exon), 49 (downstream exon)
Score: 86

ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGTGGAGATGGGAGAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 75

ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGTGGAGATGGGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGTGGAGATGGGAGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

ACTACGCTGTCGTCCTCTGCAACTACGGCCCCCGCCCTGTTCACCCGGCGGCGGCACCACTCTCGCCGCGCTCGCCGTCCTGCTCTCCTTCCACTTCCTGgtgcgtatcc ... tgttttgcagCTTGCTATGCTTTTATGGAGTTATTTTTCTGTCGTGTTCACGGACCCTGGTTCTGTTCCACCAAATTGGAATCTTGATTTTGATGTGGAGATGGGAGAAA