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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtatcttaacccatctttgtttttatctactccatcagtccgcttttcattctctctaatccgatgattgctggctggattctcacccaaatcagatctccactgccttgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAAGGTGGCTTCGGCCATGTCTTTCTTGGCCGACGTCTGACTGCCGCCCACG

Basic information

species Zea mays
transcript GRMZM2G017835_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 1
gtccgtatcttaacccatctttgtttttatctactccatcagtccgcttttcattctctctaatccgatgattgctggctggattctcacccaaatcagatctccactgccttgccttcca---gGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAAGGTGGCTTCGGCCATGTCTTTCTTGGCCGACGTCTGACTGCCGCCCACG
                           |||    | | |   |   ||||| ||| |     ||    || ||  ||  |    | |||      | |  | |  | ||  |||      |   ||| || || ||||| || || |  ||||| || ||||||||||| |||||||||||||| || || || ||| ||||||||||  | ||||  |   |||
--------------------------gtattgttttcttttattatcttttaattgtt----atattgtgcttaatgagtaatatgtcaaggtgcttat-tgtttattgatttgttaataaaaagGTTCAAGTAGGAGGCTCACCTGTCTACAAAGTAGAGAGGAAGCTGGGCAAAGGTGGCTTTGGACAGGTTTTTGTTGGCCGACGAGTCACTGGTGGTAACG

upper sequence: GRMZM2G017835_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 1
gtccgtatcttaacccatctttgtttttatctactccatcagtccgcttttcattctctctaatccgatgattgctggctggattctcacccaaatcagatctccactgccttgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAAGGTGGCTTCGGCCATGTCTTTCTTGGCCGACGTCTGACTGCCGCCCACG
                                                            |||  |  |    |        | | |   | ||   |    | |       || ||| |||||||| || ||||| ||||| |  || ||| |||||||||||||||| ||||||||||| || || || | | | || ||  | || | || || |   |
-----------------------------------------------------------gtaagtcctttcgcgaaatacaaaatgtgggcaaagctaa---tacgagtttgtggcttgcagGTCCAAGTTGGAGGCTCTCCTGTATATAAGATCGAGAGGAAGCTTGGAAAAGGTGGCTTTGGTCAAGTATATGTAGGACGGAGGCTTAGTGGCGGCTCGG
















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|87157826|gb|DY402615.1|DY402615
EST:     CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|31355100|gb|CD439457.1|CD439457
EST:     CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|6587628|gb|AW244946.1|AW244946
EST:     CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|76285882|gb|DV025450.1|DV025450
EST:     TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|148939514|gb|EC884102.2|EC884102
EST:     TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|87156136|gb|DY400925.1|DY400925
EST:     CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|148988749|gb|EE031658.2|EE031658
EST:     TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: TAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|22935602|gb|BU571877.1|BU571877
EST:     CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGGCCGCTAACGACGACGACGACACCAACACGGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
EST: gi|60345255|gb|DN212228.1|DN212228
EST:     CGCT-ACGACGACGACGACACCAACACGGGCGCCTTTCCCCGACACG                         GTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA
genomic: CGCTAACGACGACGACGACACCAACAC-GGCGCCTTTCCCCGACACGgtccgtatct ... tgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattgctggctggattctcacccaaatcagatctccactgccttgccttccagGTCCAGGTCGGAGGATCTCCCGAGTACAAGGTCGAGAGGAAGCTTGGCAAAGGTGGCTTCGGCCATGTCTTTCTTGGCCGACGTCTGACTGCCGCCCACG
                ttctcac  putative branch site (score: 2)
                                       ctgccttgccttcc  putative PPT