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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccgaccgcgtccccctcctaccgcgcatctcggattcgttagatcttgacgggatggatgaatacctggggttgagttgattttgcgcgtccctttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGT

Basic information

species Zea mays
transcript GRMZM2G004459_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------gtattccgaccgcgtccccctccta-------ccgcgcat---ctcggattcg--ttagatcttgacgggatggatgaatacctggggttgagt-tgatt--ttgcgcgtccctttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGT
                                           |    ||   | || ||| |  |          | | ||   ||| | | ||  || |  ||||   |  | | ||| |   |    ||  || || ||  || |   ||  | ||  |||||||||||||| | | ||||| ||||||||||||||||||| || || ||||| |||||||| |||||||||||  |||||||||| |||||||||||||| 
gtccgctcacctccctcgcgctagatcgcgccgcggcccgcgatgaatcgggggtgttcccttagtcggtagatttgtggatggactccgttgcgattttggccttgttcgtctcggtgattgattccatttctgtgtggttgattccatttctgtgtggatgcagCCCGGAGCACAGGGCGAAGCTGATCGCCGAGTGCCAGGCGGCGGACGCGGTGGTGCTCACGTACGCCTGCGATAGGCCCGCCACGCTGGAGCGGCTCAGC

upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------gtattccgaccgcgtccccctcctaccgcgcatctcggattcgt---tagatcttgacgggatggatgaatacctggggttga---gttgattttgcgcgtccctttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGT
                                                                  |   |  ||  |||| || | | || | ||     |||| |    |  || ||     | |||  || |    |   ||||   |||||   | |  |      ||||| |||||| ||||||| | ||||| ||||||||||||||||| | || |||| ||| ||||||||||||||||| ||||  || || || |||||||||||||| 
gtactgccccccacccgcctccccgtcgactacttcgccgaccgcatccccatcaccatcgtcgacacctcctccaggtcctccac-tgcccctcacgctagatttgcgggtgtatttttttttgttgggggatttgtggattttgattcgttgacaattc-tgaattgctgatt-cagCCCAGAGCAGAGGTCGAAGCTGATCGCCGAGTGCCAGTCGGCGGATGTGGTGGTGCTCACCTACGCCTGTGACCAACCTGCGACGCTGGAGCGGCTCAGC
















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|211518364|gb|FL160582.1|FL160582
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTAYNATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|211153242|gb|FL160607.1|FL160607
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|31361614|gb|CD445971.1|CD445971
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|78084949|gb|DV513342.1|DV513342
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|211289495|gb|FL459844.1|FL459844
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|211289494|gb|FL459843.1|FL459843
EST:     TATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: TATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
EST: gi|91053299|gb|EB163717.1|EB163717
EST:     GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAG                         CCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT
genomic: GACTACTTCCCCGATCGCGTCCCCATCACTATCATCGACACGTCGTCCAGgtattccgac ... ttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgggatggatgaatacctggggttgagttgattttgcgcgtccctttgattgcagCCCGGAGCAGAAGCCGAAGTTGATCGCCGAGTGCCAGGCAGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACACTGGAGCGGCTCAGT
                                           ctttgat  putative branch site (score: 5)
                                      cgtcccttt  CT-rich tract
                           ttgatttt  TA-rich tract