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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtgttgtacaccacgtctcaccaatgatttacttggaagctgcagctcctgaaatggtagctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG

Basic information

species Zea mays
transcript GRMZM2G371271_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G371271_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 6
gtgagttgtgttgtacaccacgtctcaccaatgatttacttggaagctgcagctcctgaaatggta-gctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG
|| |||||| ||  |||| |    | |||| ||||  |  | || | | || ||||||||||  || |    | ||||||||||||||||||||||| || ||||||||||| || |||||||||   ||||||||||| |||||||| ||||| ||||||||||||||||| |||
gtaagttgtatt--acactataagttaccagtgatcaatctagatggtacaactcctgaaattataagtaccgcagGTTGGATGGGGAGCATGTTGTGTTTGGCAGGGTGATTCAGGGAATGGATTATGTGTACGCCATTGAAGGGGGTGCTGGAACTTACAATGGCAAGCCTAGG

upper sequence: GRMZM2G371271_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA12G03540.1 (Glycine max), 3'ss of exon 6
-------------------gtgagt-tgtgttgtacaccacgtctcaccaatgatttac--ttggaagctgcagctcc---tgaaatggtagctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG
                   || ||  | | |  | ||     | | | || |  ||||   ||   || |       |   | |  ||  | ||||  ||||||||||| |||||||||||||| ||||||||  | ||||| |||||||  ||||| |  || |||||||| || || || |||| ||| || || || 
ttgaagtgtttgtatccatgtcagagtctatgcttcataggttattatcactagtttatagttatgagttatgatatcaatttacttgtaaactttccagGTTGGATGGAGAGCATGTTGTCTTTGGCAGGGTTGTTCAAGGCATGGATATTGTGTATGTAATTGAAGGGGGAGCCGGAACCTACAGTGGAAAACCCAGA

upper sequence: GRMZM2G371271_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 6
---------------------gtgagttgtgttgtaca---ccacgtctcaccaat-gat-ttacttggaagctgcagctcctgaaatggtagctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG
                     |  | || ||  |||||     | |    ||   | ||| || |||   ||    ||    |  | |   | ||| | ||||||||||||||||||||||| || |||| ||| || ||||| ||||| |  || ||| | |||||||| || ||||| || |||||||| || || |||
gttgctccatgctctagatatgaaacttctgc-gtacaagttaatgatctacatgtagatgttccttaccagtaaaagaatatccatttaaaacttggcagGTTGGATGGGGAGCATGTTGTATTGGGCAAGGTTATTCAAGGCATGGACATTGTCTACACAATAGAAGGTGGAGCTGGAACCTACAATGGAAAACCCAGG

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|33093848|gb|CF053842.1|CF053842
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|87151676|gb|DY396465.1|DY396465
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|87152956|gb|DY397745.1|DY397745
EST:     ATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTGGGATGGGGAGCATGTTGTCTTTGGCAGGGTGATCCAAGGAATGGATAC
genomic: ATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|32930654|gb|CF035466.1|CF035466
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtctcaccaatgatttacttggaagctgcagctcctgaaatggtagctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG
 gtctcac  putative branch site (score: 3)
         aatgattta  TA-rich tract