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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgacttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT

Basic information

species Zea mays
transcript GRMZM2G005849_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgact-tctatttatggcagtccc--ttac----attatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
          ||  ||   |    |||| || ||  |   |||  |  |  ||||    |||   | |   ||| |   |||     | | ||| | | || ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||
-----tcttacaaaattcaaaaggaaaagaaatcggt--aactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 3
----gcagaat---agtcattatcgcattacaaaataattcattctgactgaacccattatg--acttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
     || |||   |      |    |||   || ||  |  |      ||  |  | | |   | ||||| ||| ||||   | ||  ||||||||       ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||
tcttacaaaattcaaaaggaaaagaaattggtaactagattctatatgttggtcttactgttctagttctagttaaggcaa--cttttaattatttt-------ctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTCATCTTTAAAAGCCCACACTACCCCAATGAATTGAT

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 3
----------gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgacttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
          || | ||  ||    || | ||| |      |  ||                 |||  |    ||   | |       | ||||| || ||     ||||||  ||| || || || ||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| || || ||||| |||||      
ttatatgtaagctgcattttctgcttctc-ttagatgggtgtgaataacattatggttttgggtgatgttagcttgaagtacatttcca-attatcttgcagGAGGTCAGGT--TGTTACCTTCAGTCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCCACATTATCCTAATGA------

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
-----gcagaatagtcattatcgcattaca-aaataattcattctgactgaacccattatgacttctatttatggcagtcccttac--attatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
      |  |   | | ||   || |  |  | ||   |     | ||   |    ||  | |     |   | | ||| | || |  ||||| || ||  |  ||||||  ||| || || |||||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| |  || ||||| |||||      
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGT--TGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA------

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
gcagaatagtcattat---cgcattacaaaataat--tcattctgactgaacccattatgacttctatttatggcagtccct-tacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
    |||  | ||| |    |   |   || || |  |  || ||| | |    | |||| ||  | || ||||   |  || |   ||||  ||         |     ||| || ||  |  |||||||  | ||||| |||||||| ||||||||||| || || ||||| |||||||||  ||| ||||| |||||      
--gtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagtt-agtatg-ctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA------

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S139_11V6.1 (Physcomitrella patens), 3'ss of exon 3
---gcagaata-gtcattatcgcattacaaa--ataattcattctgactgaacccattatgacttctatttatggcagtcccttac--attatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
      |  || |  ||||  |  |   | |   || |   || |  |||  ||| |    | ||  ||  ||    |  |       || ||||||||  |    | | |||   |  ||||||||||| |||||||| || ||| | ||| | ||||| ||||| || ||||| || |||||||| |||||||| |||||      
tccctggtgtatgcaattaatgactcgtatattgtattcggttatagctgttcccttgtgtattttcatcaataatggaacggaggtgataatttttcagGTGGCAAAGAGATTCAA--TTTAGCCAAGTCGTTATGGAGGTGATGCGACAGATCGAAGGGGCCTATGCTCTTATTTTCAAAAGCCCTCACTATCCAAATGA------

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ12208 (Selaginella moellendorffii), 3'ss of exon 3
gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgacttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
                                      | |             | || | |||||  ||   | ||       |||||  |     | |  |||||  |||| |  ||||| || |||||||| ||||||||||| || ||||| || ||||| |||||||| || || ||||||||||||||      
-------------------------------------gtaagcatctgggactagtctcccatttaatgcgtcctctctttaacttttttgcagAAGCCGCGGATGTCTCGTTCACGCAAGTAGTGATGGAAGTTATGAGGCAGCTCGAGGGAGCGTATGCACTCATCTTTAAGAGTCCTCACTATCCCAATGA------

upper sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ08214 (Selaginella moellendorffii), 3'ss of exon 3
gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgacttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
                                      | |             | || | |||||  ||   ||||       |||||  |     | |  |||||  |||| |  ||||| || |||||||| ||||||||||| || ||||| || ||||| |||||||| || || ||||||||||||||      
-------------------------------------gtaagcatctgggactagtctcccatttaatgcgtcccctccttaacttttttgcagAAGCCGCGGATGTCTCGTTCACGCAAGTAGTGATGGAAGTTATGAGGCAGCTCGAGGGAGCGTATGCACTCATCTTTAAGAGTCCTCACTATCCCAATGA------

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|89758439|gb|DY687617.1|DY687617
EST:     CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAG                         GTGATGTGACGTTT
genomic: CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAGgtagtgtgtc ... acttcctcagGTGATGTGACGTTT
EST: gi|149014772|gb|EE044464.2|EE044464
EST:     CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAG                         GTGATGTGACGTTTAGCCCAGTTTGT-ATTGGA-GTCATGAAGCAGC
genomic: CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAGgtagtgtgtc ... acttcctcagGTGATGTGACGTTTAGCCAAGTT-GTTAT-GGAAGTCATGAGGCAGC
EST: gi|149081060|gb|EE170160.2|EE170160
EST:     CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAG                         GTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAG
genomic: CATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTCATGATGAACAAGgtagtgtgtc ... acttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccattatgacttctatttatggcagtcccttacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
                            cccttac  putative branch site (score: 3)
                                    ttatttttcacttcct  CT-rich tract
                               ttacattatttttca  TA-rich tract