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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtgggtgctcgcctgctcgttcttctgaatgtgcagtctgatccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG

Basic information

species Zea mays
transcript GRMZM2G044584_T03
intron # 1
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 1
lower sequence: LOC_Os08g06474.1 (Oryza sativa), 3'ss of exon 1
cctgtgggtgctcgcctgctcgttcttctgaatgtgcagtctgatccatgttgatgtcaagtactactg-tattagcacttatggtt-tttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
  |  |  |  |   ||      |    ||  ||     ||||| | || ||     | |  | |||||  | |  || |  |   | | |||  |  ||||||||||||||||||  ||||||| |||| ||||||||||||| ||||||| ||||||||||| |||||||||
-tttggtctctttagctttggacttacatgggtgcagtttctgaacaat-ttacctactaccagtactggcactgacagtcgtctctgtctgaactttgcagAAAGCACTTGCAGGATTGAGAAGGATCAATTTAGATGGGTTGAGATGGCGTGTATTTGATGCAAAGGGTCAG

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 3'ss of exon 1
cctgtgggtgctcgc-ctgctcgttcttctgaatgtgcagt--ctgatccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
   ||  |   | ||  |  |     || |||| ||| |    ||  || |  |  |||| ||| || |  | | |  ||||| |    |||||  || ||||||||||||||||||| |||||||||||| ||||||||| ||| ||||||| |||||||| || ||||| |||
ttagtttggaattgcattaatacaatttttgaacgtgaatgcactagtctac-tacatgtgaagcacca--gcactgacacttctatcatttgaactgtgcagAAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAG

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g15360.3 (Oryza sativa), 3'ss of exon 1
cctgtgggtgctcgcctgctcgttcttctgaatgtgcagtctgatccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
           | |      | ||  |  || | |  ||| | | ||   |  || | |||||||   ||| |   | |  || | |||||  || ||| |||||||||||||   |||||||||||| ||||||||| ||| ||||| | |||||||| || ||||| |||
-----------ttggaattacattaataagatttttgagtttcaacctactaaatttgaagtactg--gtactgatagtgctgttgtttgaactgagcaaaaagcacttgcagACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAG

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g15360.2 (Oryza sativa), 3'ss of exon 1
cctgtgggtgctcgcctgctcgttcttctgaatgtgcagtctgatccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
 || |  ||       | |   ||  |  || | |  ||| | | ||   |  || | |||||||   ||| |   | |  || | |||||  || ||| |||||||||||||   |||||||||||| ||||||||| ||| ||||| | |||||||| || ||||| |||
tctcttagtttggaattac--attaataagatttttgagtttcaacctactaaatttgaagtactg--gtactgatagtgctgttgtttgaactgagcaaaaagCACTTGCAGACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAG

upper sequence: GRMZM2G044584_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 3'ss of exon 1
---cctgtgggtgctcgcctgctcgttcttctgaatgtgcagtctgatcc-atgttgatgtcaagt-actactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
       | || | ||         ||||   |  |     | || ||   || | ||||    || | || |  | | ||||   |   | || ||    ||||||||||||||| || |||||| |||||| ||| || || ||||||||||| ||||||||||| || || |||
gggttatttggagatcatgaaaaaattctaaagttttatttgcctaatttgatttagatgctctgtcagtaatagaat-gcacccttaaatcttcat----gcagAAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG

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|18385121|gb|BM418320.1|BM418320
EST:     TTCCAACTGATATGGCTACGACGCCACCAGGATTCACGGGCAACCTGAAG                         AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
genomic: TTCCAACTGATATGGCTACGACGCCGCCAGGATTCACGGGCAACCTGAAGgtgagttatt ... atgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
EST: gi|13315880|gb|BG410228.1|BG410228
EST:     TTCCAACTGATATGGCTACGACGCCGCCAGGATTCACGGGCAACCTGAAG                         AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
genomic: TTCCAACTGATATGGCTACGACGCCGCCAGGATTCACGGGCAACCTGAAGgtgagttatt ... atgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
EST: gi|211282462|gb|FL053249.1|FL053249
EST:     TTCCAACTGATATGGCTACGACGCCACCAGGATTCACGGGCAACCTGAAG                         AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
genomic: TTCCAACTGATATGGCTACGACGCCGCCAGGATTCACGGGCAACCTGAAGgtgagttatt ... atgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
EST: gi|211445695|gb|FL278216.1|FL278216
EST:     TTCCAACTGATATGGCTACGACGCCGCCA-GATTCACGGGCAACCTGAAG                         AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC
genomic: TTCCAACTGATATGGCTACGACGCCGCCAGGATTCACGGGCAACCTGAAGgtgagttatt ... atgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatgttgatgtcaagtactactgtattagcacttatggtttttgatgtgcgcagAAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAG
                                        ttttgat  putative branch site (score: 4)
                                       tttttgat  TA-rich tract