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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA

Basic information

species Zea mays
transcript GRMZM2G030598_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g41020.1 (Oryza sativa), 3'ss of exon 4
gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgc-cttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
    |    |||||   |    || | | |    | |||    | ||  | || | |   |  ||       | || | ||  || | |||||  | ||||||||||||| ||||| |||||||| || |||||||||||||| |||||||| ||||| ||||| || ||||| || ||||||||||||||||||||||||
acaaagttcttatgtggcatataagtatataacctgtttccgagaatggtcctgt-tgttagcttagcagcttaatcatgatttttctcttttgataccagGGCTTGTGTTGTTGCTAATGATAAGCTACTTGTTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCTGGATCACCTATATTTAAATGTGTTAGAAGA

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G06690.1 (Glycine max), 3'ss of exon 4
gggcaacatttatgcttctaggaaatgttttctatatttggttgcat-catactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
  ||   |       ||   || |||  ||   |  |   ||   || |||  | |  || | |  | ||   ||      | | |   | ||   | |||||||||  | |  |  ||||||  |||  ||||||||||||| ||||| |||||||| |||||||| || || || |||||||| || |||    | || 
-agcctaagaagctttttgtggcaatacttgaaaagtggtgtgatattcattgtcttcaaaaggaagttgtttttcatctaacactagttatttggtgcagGGCTTGCATTGCAGTCAATGATCGACTTTTTGTTATTGGTGGACAAGAGGGTGATTTTATGGCCAAACCCGGTTCGCCTATATTCAAGTGTTCACGCAGG

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G24640.2 (Glycine max), 3'ss of exon 4
gggcaacatttatgcttctaggaaatgttttctat--atttggt-tgcatcatactttataagaagttgctgaagttataaagaaat-tgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
    || |    |  || | ||||   ||  | |    | || | | |||  |  |  | | ||||||| |    ||  |   || | |   | ||   | |||||||||  | |  |  ||||||  |||  ||||||||||||| |||||||||||||| |||||||| ||||| || |||||||| || |||    | |||
---taagaagc-tttttgtgggaatacttggcaagtggtgtgatattcattgtcttcaaaaggaagttgattgtttttcatctaactctagttatttggtgcagGGCTTGCATTGCAGTCAATGATCGACTTTTTGTTATTGGTGGACAAGAAGGTGATTTTATGGCCAAACCTGGTTCGCCTATATTCAAGTGTTCACGCAGA

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G23660.1 (Glycine max), 3'ss of exon 3
gggcaacatttatgcttctaggaaat-gttttctatatttggttgcatcatactttataagaagt---tgctg-----aagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
        |||  | ||| |  | ||  |  ||||  |||  ||| |    | ||||| |   ||   ||||      || |||| |  | |||    | | | | |||||||||||| || |   |||||   ||   |||| |||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||     | |||
-------gtttggggttccaacacattataatctaggttta-ttgaaatgcattttattaagtgtatatgctaccttcaatttattac-atattaatgtcttcgttcagGGCTTGTGTTGTGGTTGATGATCGTCTTTATGTTCTTGGTGGTCAAGAAGGAGATTTTATGGCCAAACCTGGGTCACCTATTTTCAAGTGCTCACGCAGA

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G51540.1 (Arabidopsis thaliana), 3'ss of exon 3
gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
         ||||  |  ||   |||| | | || |     |   || ||   | |  |  | |||  ||| |   |  |   |     |    ||  ||||| |||||||| |   ||||   |||  |||| ||||||||||||||||||||||||||||| || ||||| ||||| || || |||||     |  | 
--------gttattatcttac--aatgatctttagaccaact---attatggataa--aacatttgacgaaatagcatcgtgttctgtgtgccattgtagGGCATGTGTAGTAGTTGATGACCGACTATTTGTAATTGGTGGTCAAGAAGGTGATTTCATGGCTAAACCTGGATCTCCAATCTTCAAATGCTCACGCCGT

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G27220.1 (Arabidopsis thaliana), 3'ss of exon 4
gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgcctttt--acttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
               || ||   | ||| ||   |   ||  ||  |     ||| |    |||  || | | |   || |    |  |||      |  ||||||||||||||||| || |||||||| ||||| || ||||| ||||||||||| ||||||||||| |||   || || || || || ||     | |||
--------------gttttat--attgtctttagtcactgcctgttttgccttttgttttgagtcccttagggtgctaacattgcggttttacggtgtgtagGGCTTGTGTAGTTGCTAACGATAAACTACTTGTAATCGGTGGCCAAGAAGGTGACTTCATGGCCAAACCTAACTCACCCATCTTCAAGTGCTCACGTAGA

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0054g00620.t01 (Vitis vinifera), 3'ss of exon 4
---gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
     |  |  || ||| || || |     |   ||||  ||      |   |  |  ||||  || |       | |      |||    |||| | | |||||||||| | || |   |||||    | |||||||||||||||||||| || ||||| ||||| || ||||| || ||||| ||||| ||     | || 
ttctagggagtttcatggttatatg---catagactattgttctccataatttgttacataactagctcaaattttcacttttcaatgttatttttcatgcagGGCTTGTATTGTGGTTGATGATCGGTTACTTGTTATTGGTGGTCAAGAGGGCGATTTTATGGCAAAACCTGGATCACCTATTTTTAAGTGCTCCCGTAGG

upper sequence: GRMZM2G030598_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0171g00320.t01 (Vitis vinifera), 3'ss of exon 4
-----------gggcaacatttatgcttctaggaaatgttttctatatttggttgcatcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
           || |||  ||| |  ||  | | ||   ||   |||  |||    ||| ||   |||    ||||  |  | || |  |        ||| || |   ||||||||||| || |   |||||   ||  ||||||||||||||||||| |||||||| ||||| || || || || ||||| || || ||     | || 
atcaatatattggacaattttttttttttcatgcaa---ttcaaataaatgg----atcctatcctatctatagtttttctaatt-ttgattgtcaaacttctatt---agGGCTTGTGTTGTGGTTGATGATCGGCTTTTTGTTATTGGTGGTCAAGAGGGTGATTTTATGGCTAAACCCGGTTCACCTATTTTCAAGTGCTCACGGAGG

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|74234079|gb|DT641993.1|DT641993
EST:     GAGAAAGAGTGGAGGAGCGAGAAACCAATACCGCGTGGAGGTCCTCATAG                         GGCTCGTGTAGTTGCCAATGATCAACTCCTTGTTATTGGTGGTCAA
genomic: GAGAAAGAGTGGAGGAGCGAGAAACCAATACCGCGTGGAGGTCCTCATAGgtctcgaact ... ttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAA
EST: gi|76013568|gb|DT940738.1|DT940738
EST:     GAGAAAGAGTGGAGGAGCGAGAAACCAATACCGCGTGGAGGTCCTCATAG                         GGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGG
genomic: GAGAAAGAGTGGAGGAGCGAGAAACCAATACCGCGTGGAGGTCCTCATAGgtctcgaact ... ttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatactttataagaagttgctgaagttataaagaaattgccttttacttccagGGCTTGTGTAGTTGCAAATGATAAACTCCTTGTTATTGGTGGTCAAGAAGGTGATTTCATGGCCAAGCCTGGGTCTCCTATATTTAAATGTGTTAGAAGA
                                      ttgccttttacttcc  CT-rich tract
                        aagttataaagaaatt  TA-rich tract