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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcataacatcttattgtatcatggtcgaggaatcatgccttttgctggtcacgttaaaatgtgcttggtgtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA

Basic information

species Zea mays
transcript GRMZM2G044584_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g67200.1 (Oryza sativa), 3'ss of exon 1
tttcataacatct-tattgtatcatggt-cgaggaatcatgccttttgctggtcacgttaaaatgtgcttggt-gtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
    | ||||||| |||| |       | |  |   |||      |      |||  | |   |||  ||| |  ||   |||  |||| |||| ||   ||||| ||||||||||| |||||||||||||||||||| || |||||||||||||| |||||||| ||||||||||||||||| ||||| ||||| || ||||
-ggtaaaacatctatattttccttcaattctcgtcttcaaattgctaaagcttcatataatgctgttgttgcttattaagcatgcactgttctgatca--cagGACAGGGATCGCAAACTGAGGATATTTTCTGGAAATGAGCATCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCGTGAGA

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 3'ss of exon 4
tttcataacatct-tattgtatcatggtcgaggaatcatgccttttgctggtcacgttaaaatg-tgcttggtgtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
    ||||  | |   || ||| ||  ||     |  ||   |   |  | |    | | | |  | ||   ||||   ||| || || |     ||||||||||||||||||||| |||||||||||||||||||  || ||||| |||||||| |||||||| |||||||||| |||||| || || || || |||||||
--caataatctatgctttctattattttccccttaaaattgttgaaggggctttaatgatacttctactgcctgttaatcatctattgttacaaccctccagGATAGGGATCGCAAACTGAGGATATTTTCTGGAAGTGAGCATCCCTTCCATGATCGCCCTCTTGAACCTTTTGCGATGCCACCGCGTCAGGTGCGCGAGA

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 4
tttcataacatct-tattgtatcatggt-cgaggaatcatgccttttgctggtcacgttaaaatgtgcttggt-gtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
   |  || |||  |||| |   |   | |  |   |||     ||      |||  | |   |||  ||| |  ||   ||| ||||| |||| ||   ||||| |||||||| || |||||||||||||||||||| || || ||||||||||| |||||||| ||||||||| ||||||| | ||| ||||| |||||||
-ggcgaaagatccatattttcctacaattctcgtcttcaaattgttaaagcttcatataatgctgtttttgcttattaagcatgtactgttctgatca--cagGACAGGGATCGTAAACTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTATGATGCCACGACGCCAAGTGCGCGAGA

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g15360.7 (Oryza sativa), 3'ss of exon 4
-----tttcataacatcttattgta-tcatggtcgaggaatcatgccttttgctggtcacgttaaaatgtgcttggtgtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
      |  |||   || ||   |  ||||  ||||    | |       | |   | ||| |   || |||||    ||   ||| ||||| |||| ||   ||||| |||||||| ||  ||||||||||||||||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| ||||| |  ||||
caaaaatgtatattttcctacaattctcatcttcgaattgttaaagtagcttcatataacgctgttat-tgctta---ttaagcatgtactgttctgatca--cagGACAGGGATCGTAAATTGAGGATATTTTCTGGAAATGAGCACCCATTCCATGATCGCCCTCTTGAACCTTTTGTGATGCCACCACGCCAAGTGCAGGAGA

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 4
tttcataacatcttattgtatcatggtcgaggaatcatgccttttgctggtcacgttaaaatgtgcttggtgtttgacat----atactgctct--ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
||| |   |||  ||| | || |||       ||   ||  ||| | || |    |     | |||||| || || ||||    |  |  || |  | |  | |||||||| ||||| || || ||||||||| ||||  | || || || ||| ||||| | ||||| ||||||| |||||||||||| ||||||||||| || |
tttta-gtcattatat-gaatgatgtcttgttaactttg--tttagatgattcaat--gtgtttgcttgttggtttacattacaacgccactttatgtttgtacagGATAGAGATCGAAAACTAAGGATATTTGCTGGTGATGAGCACCCTTTCAATGACAGGCCTCTTGAACCTTATGTGATGCCGCCTCGGCAAGTACGAGAAA

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|16378867|gb|BI992643.1|BI992643
EST:     TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGAT                         GATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
EST: gi|33102772|gb|CF062732.1|CF062732
EST:     TGATTCGCAAAGCTGTGTTGCGCATGCTTCCCCGCAACAAACTGCGTGAT                         GATAGGGATCACAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
EST: gi|18385121|gb|BM418320.1|BM418320
EST:     TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAGACTGCGTGAT                         GATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
EST: gi|13381725|gb|BG458280.1|BG458280
EST:     TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGAT                         GATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
EST: gi|87153153|gb|DY397942.1|DY397942
EST:     TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAGACTGCGTGAT                         GATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
EST: gi|33095052|gb|CF055046.1|CF055046
EST:     TGATTCGCAAAGCTGTGTTGCGCATGCTTCCCCGCAACAAACTGCGTGAT                         GATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT
genomic: TGATTCGCAAAGCTGTGCTGCGCATGCTTCCCCGCAACAAACTGCGTGATgtaagtgaaa ... ggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctggtcacgttaaaatgtgcttggtgtttgacatatactgctctggtcctccagGATAGGGATCGCAAGCTGAGGATATTTTCTGGAAACGAACATCCATTCCATGACCGCCCTCTGGAACCTTTTGTGATGCCGCCACGGCAAGTACGCGAGA
                          gtttgac  putative branch site (score: 4)
                                               tcctcc  putative PPT
          ttaaaatgt  TA-rich tract