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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaattatgggtgataatgtatgctcagtcttcagctattcctgttgcctgttgttacatctttttttaaagaaaaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT

Basic information

species Zea mays
transcript GRMZM2G408242_T04
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 6
----tctaattatgggtgataatgtatgctcagtcttca-gctattcctgttgcctgttgttacatctttttttaaagaaaaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT
    |  | | |   ||  | || |||| | |||   ||   |   |        |     || | |||||  ||     |    | | ||  ||| |||||||||||  |||| |||||||| ||||||||||| ||||| |||||| |||| || || ||||| ||| | |||||||| ||||| || || ||| | ||||| 
caaatgaattgaattgtctttat-tatgattagtgaacataatgcacgcaaaattttcaactataccttttcctatgctta----tcatctgctgttacttgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC

upper sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 8
tctaattatggg--tgataatgtatgctcagtcttcagctatt-cctgttgcctgtt--gttacatctttttttaaagaaaaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT
 ||||         || |||| | || |     | ||  |  |   | ||    |||  |||  ||    |||   ||||| |||     | |||   || ||||||| ||||| ||||| ||||||||||||||||| || ||  || | |||||  |  |||||||  | || ||||||||||| || |||||  | |  || 
-ctaacagctatcttgctaatat-tgttggaattgcaatttctatttattagtagttttgttggattaaatttacgagaaagaacatgaatcatg---ctggcagGGGGCTTGTAAATGACACATACAAGATGGACCTAATTCTTGTACATCCTCCGCATTTGATTGCTTTAGCTTGCATATACATTGCTAGTGTGCTCAGGGAG

upper sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 7
-------tctaattatgggtgataatgtatg---ctcagtcttcagct--attcctgttgcct----gttgttacatctttttttaaagaa-----aaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT
         |   |||| |  ||| || ||    |||| |    ||||  |  | |     ||    | | |   | || | |  |||| |     |||||  |  ||  |||  || ||||||  ||||||||||||| || ||||||||||| || ||  || |||||||||||   || || || || |||||||||||||| |||||    | ||| 
gtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtg--tttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG

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|211115727|gb|FL229698.1|FL229698
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCGTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTAGTC-TCATATACCCT
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCC-TGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTA-TCCTCATATACCCT
EST: gi|211116530|gb|FL229719.1|FL229719
EST:     GTTNGT-GCAGGATGCTGGCATAACAGACCTGACACATTTTGCCTG                         GGGCCTTGTTTATGATACATACCAGATGGACC
genomic: GTT-GTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACC
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|211117330|gb|FL229739.1|FL229739
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|22818772|gb|BU498862.1|BU498862
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|5325108|gb|AI783299.1|AI783299
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGNTAATGATACATACAAGATGGACCTTATCCTCATATACCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCC
EST: gi|148937775|gb|EC881986.2|EC881986
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|6020447|gb|AW065375.1|AW065375
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGNTAATGATACATACAAGATGGACCTTATCCTCATATACCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCC
EST: gi|149084617|gb|EE174095.2|EE174095
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|26456727|gb|CA828310.1|CA828310
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|74237502|gb|DT645416.1|DT645416
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCC
EST: gi|22521612|gb|BU080423.1|BU080423
EST:     GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTG                         GGGCCTTGTTAATGATACATACAAGATGGACC
genomic: GTTGTTGCAGGATGCTGGCATAACAGACCTGACACAATTTGCCTGgtaagcactg ... tgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctgttgttacatctttttttaaagaaaaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGAT
                                aactgac  putative branch site (score: 2)
       ttgttacatctttttt  TA-rich tract