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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacccacacgactattatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 5
gtattacccacacgactat-tatacctatttgctgtcatatcccttttttta-gtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
||||||||   ||   |||  ||  || |||    |   |||  |||| | | | |  |    |  |   | | |||  | ||   |  | ||    | || || || |||||  ||||||| || || |||||||||||||| || |||||||||||||||||||||||||||||||| || |||
gtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcagATCTTCCGCAAGGAGCCATTTTTCTATGGTCATGACAACCATGATCAACTTGTTAAGATCGCAAAG

upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 3'ss of exon 6
------------gtattacccacacgactattatacctatttgctgtcatatcccttttt-ttagtatttcttgtgattc--cttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
              |    | | |   | ||  | | |  ||       | |  |  |   ||  | |   || || ||    || |   | |||      |||| |   | |    ||     || |||||||| ||||| ||||||||||| ||||| || ||||||||  ||||||||||||| ||||| || |||
gtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtga----attgaagtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG

upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtattacc-cacacgactattatacctatttgctgtcatatccctttttt---tagtatttct-tgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
     ||||   | ||    | | | | ||  || |   || || | |  ||||    |  | | | | || ||||  ||              | |   | |  | |  | ||   || |||||||||| ||||| ||||||||||| ||||| || ||||||||  ||||||| ||||| ||||| ||||||
gtaacgtatcctcgcagtttattttaacactaatctttcgttatttacagttttcccatgatgtgtatctgcgattttttcattctgaagtacttctcgttatgctgaagagattgcgt-ggttgcagATCTTTCGGAAGGAGCCATTCTTTTATGGACATGACAATTATGATCAGCTTGTGAAGATTGCCAAG

upper sequence: GRMZM5G845755_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 5
gtattacccacacgactattatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
    ||   | | |  |  ||||  |      |  ||| | | ||  |  ||    |  |   ||     |    || |    | |     |    || ||| || |  |  ||| ||||||| || |||||||| ||||| || |||||||||||  ||||||| ||||| ||||| || |||
---gtaagga-atgtattctatattttgaattttgcatgtacattcctgaagcccattatcccataatgaaccagcaggttgcaaacctgacaggctaccatttgtt--taattgtagATTTTCCGCAAGGAGCCGTTTTTCTATGGTCATGACAATTATGATCAGCTTGTCAAGATCGCTAAG

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|60350778|gb|DN217751.1|DN217751
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     GATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: GATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccttatagacatgaccaatattaatctatttatcatatgctgttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG
                     tattaat  putative branch site (score: 2)
                   aatattaatctattta  TA-rich tract