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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgaacattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaatatagctgacttggttacttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC

Basic information

species Zea mays
transcript GRMZM2G056975_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 5
-atttgaacattatgtggttgctttgtgctgcat-caaa-taaatgagcaattttatcagtgaatatagctgacttggttacttgtattg-tttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
 | |||||   | ||  |  | | |||  ||||| |||| || || | ||   |     |      | ||||| |||  |||||  |||  |||| ||||  |||||||||||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |
gaattgaatgct-tgctgaagttctgta-tgcatgcaaactacattaccagaatc--tggcaccacttgctgatttgcctacttaaatttctttgctctgccagCCTACAGTTGCTGCAATTGAAGCTGGGAAAGATATAGCATTGGCGAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACAAAAGC

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 5
atttga-acattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaatatagctgacttggtt-acttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
 | | | | |  |     |    |        ||   ||   |   || ||  |||||  || | |  | |    | | |  |    |  || || |||||||| |||||||| || || ||||| || ||||||||||| ||||| |||||||||||| | ||||| || ||||||||||| ||||| ||||| || || |
gtataagaaaacagaaaatccactaactaaatatggtattggttgtcagtt--atcagacaacagatattagaaagctgaaatcctctcattattttgttagCCAACAGTTGCAGCGATAGAAGCAGGGAAAGACATAGCTTTGGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 5
attt--gaacattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaatatagctgacttggtt-acttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
 |||  |||||       |   ||   |   | ||   ||  ||   ||   |||||||  || | |  | |    | | |  |    |  || || | |||||| ||||||||||| || ||||| || ||| ||||||| || || |||||||||||| | ||||| || ||||||||||| ||||| ||||| || || |
gtttaagaacacagaaaagacactaactaaag-atggtattcattgtca--cttatcagacaacagatattagaaagctgaaatcctcttattattttattagCCAACAGTTGCTGCGATAGAAGCAGGGAAATACATAGCTTTAGCCAACAAAGAGACATTGATTGCTGGAGGTCCTTTTGTTCTTCCTCTTGCTCAGAAGC

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 5
atttgaacattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaat-atagctgacttggttacttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
    | | ||  | |  ||  ||  |  |  | |  || ||   |  ||   |  ||  | |   || |||    | |  |||  || ||| | |||  ||||||| ||||||||||||||||| || || ||||| ||  | ||||||||||||||| | || |||||||||||||| |||||||| |||||  ||||||
----gtatatactctaattttttgttattaaaccttattaagaggatatgaaaaaagaaagttgcagatgataaagcttgttgc-ttatttttactgc-agCCTACGGTTGCTGCAATTGAAGCAGGAAAGGACATTGCTCTTGCAAACAAAGAGACATTAATCGCAGGTGGTCCTTTCGTGCTTCCGCTTGCCAACAAAC

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 5
-atttgaacattatgtggttgctttgtgctgcatcaaataaatgagcaattttatcagtgaatatagctgacttggttacttgtat-tgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
   ||||   |  | |    |  ||       |  || |  || || || |  ||||  ||  | ||         || ||| | | | | | ||   |||||||||||| |||||||| ||||| || ||||||||||| || || ||||||||||| || ||||| || ||||||||||| ||||| ||||||||||| |
tccttgattttcttattaaggacttaaatgtaaataattggataagaaacta-atcaa-gatgacagtctgaaaattttcttctgtgtctgtttttcattagCCTACAGTGGCTGCAATAGAAGCAGGGAAAGACATAGCCTTAGCCAACAAAGAGACCCTAATTGCTGGGGGTCCTTTTGTCCTTCCTCTTGCACACAAGC

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S73_243V6.1 (Physcomitrella patens), 3'ss of exon 7
atttgaacattatgtggttgctttgtgctgcatc-aaataaatgagcaattttatcagtgaatatagct--gacttggttacttg--tattgtttgttctgtt--agCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
          ||| |    |    |  || |||| ||||  |  |  | | | |  ||   |||  | |  |||  ||||  ||   |   | ||  | ||||  |||| ||||||||||| ||||||||||||||||| || || ||||| |||||||||||  | ||||| || ||||| | |||| | || || ||  | || |
-------gtctatttctaagtacaggtctacatctaaatcgacaaatattatcagtaggtgataacgtttggacgaggttttttaattgaaggtttgtttgttgcagCCCACAGTTGCTGCTATTGAAGCTGGTAAAGATATTGCCTTGGCCAACAAAGAGACTTTGATTGCTGGAGGTCCATATGTGTTACCTCTGGCTAAGAAGC

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|13125884|gb|BG316454.1|BG316454
EST:     CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
genomic: CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAGgtaatgcctt ... gttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
EST: gi|71445035|gb|DR826085.1|DR826085
EST:     CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
genomic: CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAGgtaatgcctt ... gttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
EST: gi|14206809|gb|BG840487.1|BG840487
EST:     CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
genomic: CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAGgtaatgcctt ... gttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
EST: gi|211496438|gb|FL049443.1|FL049443
EST:     CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
genomic: CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAGgtaatgcctt ... gttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
EST: gi|149066676|gb|EE286811.2|EE286811
EST:     CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAG                         CCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA
genomic: CAGATGCAGTTACAGTTGTCACAGGGATAGTAGGTTGTGCAGGGCTGAAGgtaatgcctt ... gttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattttatcagtgaatatagctgacttggttacttgtattgtttgttctgttagCCTACAGTTGCTGCAATTGAAGCTGGTAAAGACATAGCATTGGCAAACAAAGAGACACTTATTGCAGGTGGTCCTTTTGTGCTTCCCCTTGCACACAAAC
                   agctgac  putative branch site (score: 3)
                                          tttgttct  putative PPT
            tgaatata  TA-rich tract