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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT

Basic information

species Zea mays
transcript GRMZM5G814310_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
------------gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
            ||   |  || | |||||| |||||||| || | |  || |   | ||   |||   ||        |||    || |   ||   ||    |||| ||||||| ||||||| ||||| ||||||||||| || ||||| |||||||||||||| ||||||||||| || ||||||||||| || || ||||        
catttaacatttgcaactttcaagcatgcat-tatcagaattgttgtcatgcatagcaaa---ttcggtctgtctgaattta----ctgaattttgtgtc----ctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG--------

upper sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtagg-acgaa-attttcaagctaatcattct-taaatacttatccttaaatctt-tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
    ||    | |||   |  | ||| |   ||  |   |    | | | ||||  | | |  |  | |     ||  | || |     | || |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | ||||        
----gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgtggtccagcgtatgataatacaagtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG--------

upper sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
---gcgggtagcatgaat-gcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
        || |  ||   | |||| | | | ||  || ||   |    |     ||   |   | | |     |||   | |  | |    | |   || |||||| || ||| | ||||| ||| |||||||||| |||||||| |||||||||||  |||| ||||| || || |||||||| ||| | || |        
tcttttaatatctggaccagtatctgttacacattttcatgcacatt-tgtggggttgtggtccagcgtatgataatgagtgtgttca---ttgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG--------

upper sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------------gcgggtagcatgaa-tgcatctatcagaaatgatcttgtg--taggacgaaattttcaagctaatcattc--ttaaatactta-----tccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
                                       |  |||||   | | |    |  || ||||       | |   || ||||     ||    |||  |  |||| | |     || |    ||  |   || ||||||  ||||| | ||||||||| ||||||| || || |||||||||||||| || ||||| |||||||| || |||||||||||| | ||||        
gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG--------

upper sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctt--tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
  |  |    |      | |  |     ||    ||  | |  |  |  ||     |      ||| | |       | ||||    |||     ||| ||| ||| ||||  || ||||||||||||||||||| |||||||| || || |||||  ||| |||||| || ||||||||||| |||||||| |        
--gaatttttttctgtaagcggttgtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccattttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG--------

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|71435715|gb|DR816765.1|DR816765
EST:     TTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAG                         TGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA
genomic: TTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGATGATCAGgtaatggttt ... tgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT
          agctaat  putative branch site (score: 3)
                                         tctttgcttttc  putative PPT
             taatcattcttaaata  TA-rich tract