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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 15
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatag-tactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctct----ttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                |||        |  ||||| | | |||| ||  ||   | || | | |   ||    | | ||  |   || || || |  |||||| | |  ||    |  |||| |||||||||||||| ||||| ||||||||||| || ||||| || || ||||||||||| |||||||| |||||||| ||||| |||||||| ||||| 
--------------------------------------------------------------------------------tcattaatgttattttatggtcgctactgcctagtggttttccagttagctaaa---atattttca---ttcagtactagctctaaactgtaccttatatcctcagATTGATCAAGGAGATTCGGTCAGATGTTTCTGATGTGGTTGCCGCAGATGAGTTTGAGTATAAGGATCCTGTTGATGGTTCTGTCTCCAAGCATCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                 |     |    ||   ||  |   ||| ||  |  |   |    |     ||| |||  || || |   |      || |||||| | || ||||  || |   | || ||  |  | || |     || || ||||| |||||||| |||||||| ||||||||||| || |||||||| || 
------------------------------------------------------------------------------------------------gtatctctctctccacttaatttcaaatccattcctttttacttgtatgactttcagactcacgtttttgga--taattggtcagGATTATAAAGGGAATTCATCCAGAGGTGGCAAATGTTGCAAGCGCAGATGAGTTCGAGTACAAAGATCCAGTAGATGGCTCTGTTTCAAAGCACCAAGGG

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S4_12V6.1 (Physcomitrella patens), 3'ss of exon 16
gtaagtggaactttt-tcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagc--aatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
|||| |    |  |  |    ||     |  ||||||| ||    |||        ||      |  |   |  |    ||         |    |  ||| |    || | | |  ||   | |   |      | | ||  ||     | |    |   |||     ||   |||    ||| ||||||||||||||  |  |||||||| | || ||    | |||||||||||||||||| ||||||||||||||                         
gtaacttccgcactcattttgtgccactgcttctcaaattta---tttccgtgtttattgtgtggcgcattcaagc-cgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagAGTGTGATTTGTGGATCTGACCCAGCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGA-------------------------

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S168_70V6.3 (Physcomitrella patens), 3'ss of exon 16
gtaagtg--gaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtcca--agtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
||||||   ||| |  ||    ||||       |||  | ||  ||   |   ||| |  ||||  | || |    |  | | | | | | ||   ||| |   |  |      |||  ||| |   ||    |||| ||     || | |  | | |||  | |  |   |    ||   ||||  |||||||| ||||| |  | |||||| |||| ||    | ||| |||||||||||||||||||| ||||||||    || |||||    || ||||| 
gtaagtttcgaattcgttt---tgtagcactgcctctgatttatacgggtc--aactaattccagcaataattttctagaaaaaacga-tgcatgtaatcac--tgcttagtgtgtgcttatctttctttttccaattgc-----tgcattggtcacaactctataca---ttctgctggctcagTATGATCAAGAAGATCAGACCAGATGTTGCTGAGGTTCAAGAAGCAGACGAGTTTGAGTACAAGGACCCAGTTGACCAGTCCGTGTCTTGTCATCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 16
gtaagtggaactttt-tcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagc--aatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
|||| |    |  |  |    ||     |  ||||||| ||    |||        ||      |  |   |  |    ||         |    |  ||| |    || | | |  ||   | |   |      | | ||  ||     | |    |   |||     ||   |||    ||| ||||||||||||||  |  |||||||| | || ||    | |||||||||||||||||| ||||||||||||||    ||  | ||||  |||||||| 
gtaacttccgcactcattttgtgccactgcttctcaaattta---tttccgtgtttattgtgtggcgcattcaagc-cgtagtggtccaggtggctgttgagaaatgtcgcttattaatgcaattctgaatttgcttgtaatttttgtactctgctcagagtgtgatttgtggatctgacccagCTTGATCAAGGAGATTAGACCTGATGTTGCCGAGGTTCAAGAAGCTGACGAGTTTGAGTATAAGGATCCAGTTGACCAGTCCATATCCAGCCACCAGGGT

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 14
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                                |||    ||| ||        | ||    ||    ||     ||  |||    || ||        |||  |  |    | ||| || ||||||||  |||   |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || 
----------------------------------------------------------------------------------------------------------------gtaagcctcagttt---tttccccaggggtgggtcttccctgacagtgt---gagcatg-------cagAATAGTGTCAGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 15
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 14
gtaagtggaactttttcaaatgtacaggaatctcaaacttgaactttttagaaccatgtccaagtactcccgtgtatatatcaacttcagaaaattatgatagtactcccgtgtatatatcaattcaagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                                                                                                |||    |||  |        | ||    ||    ||     ||  |||    || ||        |||  |  |   || ||| || ||||||||  |||   |    | ||| ||||||||||||||||| |||||||||||||| || ||  | |  ||||| || 
----------------------------------------------------------------------------------------------------------------gtaagcctcaggtt--ttttccccaggggtgggtcttccctgacagtgt---gagcatg-------cagAATAGTGTCGGGGATTCGATCTGATGTCGCTGGTATCAAAGAAGCAGACGAGTTTGAGTACAAAGATCCAGTTGATGGTTCCGTCGCAAGCCACCAAGGA

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|78108858|gb|DV527275.1|DV527275
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|71426274|gb|DR807324.1|DR807324
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|5296174|gb|AI782854.1|AI782854
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|211541121|gb|FL006422.1|FL006422
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|32906153|gb|CF010966.1|CF010966
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|5895776|gb|AW037022.1|AW037022
EST:     AGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: AGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|78024768|gb|DV493155.1|DV493155
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|31357336|gb|CD441693.1|CD441693
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|67020139|gb|CO448888.1|CO448888
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|32914018|gb|CF018830.1|CF018830
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTTTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|211190026|gb|FL186116.1|FL186116
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|149060808|gb|EE157260.2|EE157260
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
EST: gi|44900765|gb|CK827310.1|CK827310
EST:     CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAA                         GTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA
genomic: CTGATGGCAAACCTAGTAAGCATGCAGTCATCACTTTCTGATGTTAACAAgtaagtggaa ... tctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaatcgcaaacttgaactttttagaaccatgtctaaagtatctctttgtcagGTTGATCAAGGAGATCCGGTCTGATGTTTCTGAAGTAGTTGCAGCTGACGAGTTTGAGTACAAGGATCCAGTTGATGGCTCTGTGTCCAAGCACCAGGGC
                                 gtctaaa  putative branch site (score: 3)
                                           tctctttgtc  putative PPT
                 aacttttta  TA-rich tract