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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC

Basic information

species Zea mays
transcript GRMZM2G079080_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtagtc-----agactctccgtactatactggaatgactgatgtgtg--agtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC
   |  ||  |   ||  | ||  |   ||    ||||||   ||||| || |      ||  | |||    | ||||| |||||||||||||||  ||||| ||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
---acttggatcagcaaat-attctgtctg---tagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgtgagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 19
atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtag-tcagactctccgtactatactggaat---gactgatgtgtgagtttgc-cagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
  |    |||  |  |   |      |||     ||   | || |||| ||  ||  |  |||  |  | | ||  |||   |  |  ||| |   ||    ||||| |||||| | || ||||| || ||||| || |||||||| ||||| ||||||||||| | ||| ||| | ||||||||||| || || || ||     
--ctcaagatcttggaaagtggaaagctt---ctagctacctgagaatataaatctaaacctctctgatttgcttcaattatggttcctgtttctcttcatgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
--atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtga-gtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC
  ||      | |   |  | ||| ||       | |  | |||   |||||       |     |||  || |         || ||| ||   |||  ||||| || ||||| || || ||||| || ||||||||||| |||||||||||||| ||||| || || ||| |  | || |||||  | ||||||||
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtg---tagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 20
---atcatgtgattgtacagcttatggtacttggatc--agtagcatgggaatgtagtcagactctccgta-ctatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
   |   |   ||| || | ||     |||| | |||  || |  ||   ||  |  |     | ||| || |||| |     |   | || |     |    ||||| || ||| |||| ||||| || |||||||| |||||||| ||||| ||||||||||| | ||| ||| |  |||||||||| ||||| || ||     
cccagagtaaaattctagatct-gctttactagtatcttagaaaaatctaaacct--ttgatttttccttaactatgcatactttttttatat---tatcattcagGGTACTAGTCGGCCAGCTCATTATCATGTCCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTCTGACAAACAATCTTTGTTATACATATG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 11
atcatgtgattgtacagct-tatggtacttggatcagtagcatgggaatgtag--tcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
   ||  |  ||| |   | ||||| |||||  |   |   ||| | || ||     | ||  |    | |  | ||   |   || |       |    ||||| |||||| | || ||||| || ||||| || |||||||| ||||| ||||||||||| | ||| ||| | ||||||||||| || || || ||     
--tataagtatgtcctattatatgg-acttgtttgttttttatgagcatataaatctaaacctttatgattcaattgtggtttttgtttctattatcatgcagGGTACGAGTCGTCCAGCTCATTATCATGTTCTGTGGGATGAAAACAACTTCACAGCAGATGGAATTCAGTCTTTGACAAACAATCTCTGTTATACATATG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 19
--atcatgtgattgtacagct-tatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
  |  |    | | |  |  | |  | || |  || |  |  | |    ||  ||  | | |      ||| |       ||  || ||| |||     | ||||||| || |||||||| || |||||||| || ||||| |||||||||||||||||||| |  || ||  |  |||| ||||| || || || ||     
gtacgaaacaactatcgaaatatccgttaatatgaccttttccgtaactatacagataaaatg---acactgttt----gtgtttgttgtatgat----ctagGGAACAAGCAGGCCTGCACATTACCATGTTCTTTGGGACGAGAACAATTTCACAGCAGATGGTATTCAATCTCTGACTAACAATCTCTGTTATACCTATG

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 17
atcatgtgattgtacagcttatggtacttggatcagtagcatgggaatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgc--cagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----
| ||     ||    ||  | |  |   |   |   || |       ||   |||||   |  | | |  |   || | | |  | | |   ||||   ||||| || |||||||||||||| ||||||||  | |||||||||||||||||||||||||| | ||| ||  | ||||| ||||| |||||||||||     
aacactcactttaggaggctctcatttgtcagtttctaactaacatgtgctttcagaacttttggaatggat--gagtcattattttctttctttgtggcagGGGACAAGTAGGCCTGCTCATTACCATGTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATG

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|6021559|gb|AW066487.1|AW066487
EST:     GCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG                         GGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTC
genomic: GCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAGgtaaaagtaa ... agtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtagtcagactctccgtactatactggaatgactgatgtgtgagtttgccagGGAACGAGTAGGCCTGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC
                                 gactgat  putative branch site (score: 3)
                   tactata  TA-rich tract