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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcattatgtcatttcatattttcatgaactttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG

Basic information

species Zea mays
transcript GRMZM2G110834_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 4
---atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcattatgtcatttcatattttcatgaactttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
   | ||  |||     |   |   |   ||| ||  ||||    ||| |   ||  ||||||    |||  ||| |||| | |  |  ||||  | |||||||| |||||||||||||||||||| |||||||||||||| |||||||||||||| |
gagaattgtgcatcattggtcttgtta-taaatatcataaaagagagaacaa-aacctgtagtttgcatgggatt-catactctgttccacttaatcttgcagACCCGTGATGATGCTAGGCAATTTATGAAGTATCTTCACCCTGATCTTGGTGTTG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 5
atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcgg----caaaatgt-agtcattatgtcatttcatattttcatgaactttgttt--tgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
        || |  | ||||  | |||  |  ||        ||  | |    ||    || | | |   ||   |  |||   |||   |  |||  |   | ||||  |||||||||||| | || || ||||||| |||||||||||||||||| || |
-------taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 7
atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcatta-tgtcatttcatattttcatgaactttgttt-tgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
   |||     |     | ||    |  ||   ||           |  ||  | ||   |   | |||  |  ||| | |||   |  |||||   | ||||  |||||||| ||| | || || ||||||| ||||||||||||||||||||| |
--gtcattgtcttctgttgcataatcttagtcatttgttgctctgtctccagcaagtgaacgaaagtgtactaacatgtattctcaatttttgtccctacagAAGCGTGATGACGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGTGTTG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 5
---atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcatta-tgtcatttcatattttcatgaa-ctttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
    |||   |       | |||  || ||   ||| |   ||     |     |  |  ||| |  | | |   |     | ||  |||| || |  ||| ||||  |||||||||||| ||||||||||||||| ||| ||||||||||||||||| |
tgtgtttttcc---ctgaatttccttgacaccaattatg--gatctttggtatgatttccagttaaaagtattgatagtagtctttctgaatctctcatttccagAAACGTGATGATGCTCGGCAATTCATGAAGTTTCTCCATCCTGATCTTGGTGTTG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S159_14V6.1 (Physcomitrella patens), 3'ss of exon 4
-atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcggcaaaatgtagtcattatgtcatttcatattttcatgaactttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
     |||  | |      | | |     || | | |   |     ||       || ||| ||   |    || |  | ||  |        | | ||||| ||||||||||||| |||||||  |||||||| | ||||| |||||||| ||| 
gcaaacagtgactgtctgattatttcttcagttctgagttaacttggctttgctttg-agttatacagcttgttgaactgttttttcttcgcatgtggcagAATCGTGATGATGCTCGGCAATTTTTGAAGTATTTGCATCCGGATCTTGGCGTCC

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|74240999|gb|DT648913.1|DT648913
EST:     ATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG                         ACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGT
genomic: ATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAGgtgaatgcag ... tgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGT
EST: gi|76910093|gb|DV163697.1|DV163697
EST:     ATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG                         ACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGT
genomic: ATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAGgtgaatgcag ... tgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcggcaaaatgtagtcattatgtcatttcatattttcatgaactttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
                                          ctttgtttt  CT-rich tract
                        atttcatattttcat  TA-rich tract