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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttctttggtccaacatagcttgtctccagtaatacaggagtggatgtggatatttttgtagtgattgacccagtctaatatcttatctttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC

Basic information

species Zea mays
transcript GRMZM2G105253_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105253_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 2
gttttctttggtccaacatagcttgtctccagtaata--caggagtggatgtggatatttttgtagtgattgacccagtctaatatcttatctttctt----gcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC
      | || |  |  |   | |  ||  |  | |       |   | |   ||||| | | |   | |  || ||   |||  |||| | ||| ||    |||||||||||||||||||||||||||||||||||||||||| ||||||||||| || |||||||| || || || || |||||||||||||| ||||| ||||
-----atgtgcttaatgagtaccttcctaaaagagttgttcttaactggtaatgatatctctctga-gttccacacatagtaacctcttcttttttttttctgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATATATAACAGCTGAACAATTCTCACCGGAGTGCCTCCTCGATTGCTTGGATCTGTCATCAGAAC

upper sequence: GRMZM2G105253_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 3
gttttctttggtccaacatagcttgtctccagtaatacaggagtggatgtggatatttttgtagtgattgacccagtctaatatcttat-------ctttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC
   |   ||| |   |  ||| |||     | | || |   |    |||     | ||   |   || |||    |  |  | |  | |       ||    |||||| ||| ||  ||||  | || || ||||| || ||||||||||| || || |||||||| || |||||||| || |||||| ||||||| ||| | || |
--atctcttgat---aggtag-ttggaattattgattcttaaaaatatgctagaacttgc-tgaagactgaaatggctttgtgttcttttggacaactgaaatgcagAATGGAAAGGCTTGTCTAGGGGATATAATCTATCGATACATAACGGCAGACCAGTTCTCGCCTGAATGTCTCCTTGATTGCCTGGATCTTTCAACAGAGC

upper sequence: GRMZM2G105253_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 4
gttttctttggtccaacatagcttgtctccagtaataca-ggagtggatgtggat-----atttttgtagtgattgacc-cagtctaatatcttatctttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC
      ||| |  ||||||   |  ||   |  | || | ||| || || | | |     ||||  ||  |  |||    |  |  | |     ||     || |||| ||| ||| | ||  ||||||| || || || || ||||| || ||||| |||||||| ||||||||||| || |||||| |||| |||||||| ||||
------ttttgaacaacatta-taatcatgaagagtatatggaatgcatcttgtttttcaatttcagttttatttggtagctattcattgctcaattgccattacagAATGGGAAAGCATGTCTGGGTGATATCATCTATCGCTACATCACTGCTGAACAGTTCTCCCCAGAATGTCTCCTTGATTGCCTGGACCTATCATCAGAAC

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|26457008|gb|CA828591.1|CA828591
EST:     TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAG                         AGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG
genomic: TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAGgtaaaatact ... tttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG
EST: gi|76288447|gb|DV028015.1|DV028015
EST:     TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAG                         AGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG
genomic: TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAGgtaaaatact ... tttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG
EST: gi|21891658|gb|BQ744871.1|BQ744871
EST:     TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAG                         AGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG
genomic: TGCTCGCAGAGATGGAAATCCCCGAAATGTACCTGGAGACACTGCCCAAGgtaaaatact ... tttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtggatatttttgtagtgattgacccagtctaatatcttatctttcttgcagAGTGGTAAATCTTGCTTGGGTGAGATAATTTACCGATACATAACAGCTGAGCAGTTCTCACCAGAATGTCTACTGGATTGCTTGGATCTATCATCGGAAC
                              gtctaat  putative branch site (score: 3)
                                    tatcttatctttctt  CT-rich tract
                                 taatatcttatcttt  TA-rich tract