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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaatattatttaaaaaagaagtttgatttttcccagtatcctgatttcattttaaatgtatgtatacatgagcttacaagtctttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA

Basic information

species Zea mays
transcript GRMZM2G126361_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 1
cacaatattatttaaaaaagaagtttgatttttcccagta---tcctgatttca-----ttttaaatgtatgtatacatgagcttacaagtc-tttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA
          |||   || |  | | || ||||||   |    |||  |||| |     |||||  ||||   |  |   || ||||||| | | || || ||  |||||| |||||  ||||||||||| |||| |||||||| || ||||| ||||||||  | || ||||||||||||||||| ||||| || |||||| | ||||
---------ctttctgaatgctgatcgacttttccttatggcttcccaatttgataagcttttatctgtaccaaagcgcaagtttacaagacatgttattgtctgatagGTTCACTCGAGAGGAAAGGCTCTGGCAAAAGATGTCGACTTTGAGAAAATTGCCCGGAGAACCCCTGGTTTCACTGGAGCTGATCTTCAAAACTTGATGA

upper sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 1
cacaatattatttaaaaaag--aagtttgatttttcccagtatc--ctgatttcattttaaatgtatgtatacatgagcttacaagtctttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA
 |       ||||   |     | |||||  |       || ||   ||||||  |||   |  | ||| ||  ||   | |  |    || | | |||    ||| || ||  ||||||| ||  | || || |||||||||||||| ||||||||||| || |||||||| |||||||| ||||| || || ||  | ||||
gattggtgcatttggtaggtccacgtttgtatgcaatgtgtctcgattgattttgtttcgtacatttgtgtatctggattaatcaactcttctctctca----gGTGCATTCTAGAGGAAAAGCGCTTGCAAAGGATGTTGATTTTGAAAAAATTGCTAGGAGAACCCCTGGATTCACTGGGGCTGATCTGCAGAATTTGATGA

upper sequence: GRMZM2G126361_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 1
cacaatattatttaaaaaagaagtttgatttttcccagtatcctgatttcattttaaatgt-atgtatacatgagcttacaagtcttt-ttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA
     |  | || | |   |   | | |   || |  || |    ||    || |     | ||   ||  |     ||   |  ||  ||||||    ||||| || ||  | || |||||  | |  |||||||| || ||||| ||  |||| |||||||||||||||||||| ||||||||| | |||||||| ||||
----gttcttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttatt--ttagGTTCATTCTAGGGGGAAGGCACTCGGTAAAGATGTGGACTTTGACAAGGTTGCCAGAAGGACCCCTGGTTTCACGGGTGCTGACTTACAAAACCTGATGA

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|93283832|gb|EB676096.1|EB676096
EST:     AGGTCACCGTTGACAGGCCAGATGTTGCCGGACGCGTCAAGATTCTTGAG                         GTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATT
genomic: AGGTCACCGTTGACAGGCCAGATGTTGCCGGACGCGTCAAGATTCTTGAGgtcagtgatg ... tatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcattttaaatgtatgtatacatgagcttacaagtctttttttatcaaatagGTCCACTCCCGAGGAAAGGCTTTGGCGAAAGATGTTGATTTTGATAAAATTGCTAGAAGGACCCCTGGTTTCACTGGTGCTGACCTCCAAAACCTCATGA
                           agcttac  putative branch site (score: 3)
                                     tctttttttatc  putative PPT
     attttaaatgtatgta  TA-rich tract