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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAA

Basic information

species Zea mays
transcript GRMZM5G879882_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 9
gtaagtttccctgcatacaaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAA-----------
                               ||||    |||   | | | |    |      ||  |   |||||   |||||  |||||||||||  |||||||| |    | ||    | |   |||||| |||||||| |||||||||||||||||||           
------------------------------attcacatattcctcatgtgaatccatgatgaatttctaacttttt-tgttttagttatttcattatactgtccttattccttttctatggtacct-tgcagGGTTTATTGCAATGTATGCTACTCTTGCAAGCAGAGACGTG

upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 9
------------gtaagtttccctgcata-caaactgaagaatgttcatgctttctcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGC----TACTCTTGCAA--------------------------
             | |   |  ||||  | ||||   |  |    ||  ||| |||  ||   |||| ||||   ||       | || |||||| |  |     ||| | | | | |   ||  |  ||| |  || |      |  || |||||   |   |     || |||  |                           
ttatcattaatcatgacagtttctgctgagcaaaacaagaagaaatctagctatcttgaat--tagttgtttacagtcaccaaatattgacatttca--tgcagGATT-TATCGCCATGTATGCAACTCTTGCCAGCCGTGATGTGGATTGTTGCCTGATTCCCGAATCACCCTTTTACCTGGAGGGTCCAGGAGGCCTGTTGGA

upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 9
--gtaagtttccctgcatacaaactgaagaat------gttcatgctttc--tcaaagcgtagtagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTAT----GCTACTCTTGCAA--------------------------
    |||  |  |||  || ||  | || | |       || | ||| |     |||  |   | | ||| | |    ||| ||||  | ||    ||    ||| | |||   |   ||  |  ||| |  |  ||  |  |  || ||||    |      |  || |||  |                           
agaaaagaattgctgt-tataagttcaaaagttattccattgaagctgttagcgaaattgattttgcttcatatatgctttattttggacttatgatacagGATT-TATTGCAATGTATGCTACTCTTGCGAGTCGAGACGTGGATTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTCCTGGTGGACTCTATGA

upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G15170.4 (Glycine max), 3'ss of exon 9
--gtaagtttccctgcatacaaactgaagaatgttc-----atgctttctcaaagcgtag--tagtttcttgttgttttttttttacattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTAT----GCTACTCTTGCAA--------------------------
    |      |  | ||   |    ||   | |||     |   | ||   || | |    | | ||| | |    ||| ||||  ||||    |     ||| | |||   |   ||  | |||| |  |  ||  |  |   | ||||    |      |  || |||  |                           
gaaaagaacggctagtatgatattcaaaagttcttccattgacattgtcatcaaacttgactttgcttcatatatgctttattttggatttatgatgcagGATT-TATTGCAATGTATGCTACACTTGCAAGTCGAGACGTGGACTGTTGCTTAATTCCAGAGTCACCCTTTTACCTTGAAGGTACTGGTGGACTCTATGA

upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 9
-------------gtaagtttccctgcata-caaactgaagaatgttcatgctttctcaaagc----gtagtagtttcttgttgttttttttttacattttaactatt-tcat-tatgttgtccttact----gtgatact--tccttgcg-gatgcagGATTTATTGCCATGTATGCTACTCTTGCAA-----------
              | |   |   |||  | ||||   |  |    || |||| |||  ||      ||   |||  |    | ||    ||| |      |  |||   ||| ||||     ||| |     |||||  |  |  ||||  ||| |  || | |      |   ||           |           
tttatcattaatcatgacagttgttgctgagcaaaacaagaagaaatcttgctatcttgaattagttgttacagtgaccaaatattgacatttcatgcagGATTTATCGCCATGTATGCAACTCTTGCCAGCCGTGATGTTGATTGTTGCTTGATTCCAGAATCACCCTTTTACCTGGAGGGTCCAGGAGGACTGTTGGA

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|14208413|gb|BG842091.1|BG842091
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTTGCAA
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAA
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG                         GATTTATTGCCATGTATGCTACTCTTGCAA
genomic: AAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTGgtaagtttcc ... gcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttaactatttcattatgttgtccttactgtgatacttccttgcggatgcagGATTTATTGCCATGTATGCTACTCTTGCAA
                        tccttac  putative branch site (score: 2)
                                      cttccttgc  putative PPT
     taactatttcattat  TA-rich tract