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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcaacttttactctcaaatcggcatttgatattcttattatcatcattcgtaccagtctgagcacacttgtttctcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAAC

Basic information

species Zea mays
transcript GRMZM2G139038_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g41100.6 (Oryza sativa), 3'ss of exon 6
-----gtgcaacttttactctcaaatcggcatttgatattct-tatt-atcatcattcgtaccagtctgagcacacttgtttctcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAAC
     |||| |||  || | |    |      || ||||  |  ||| ||  | |       || ||||||||||| |||||    | |||||||  |||||||||| | |||| || | ||  | ||||||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| |||||| 
gtaatgtgctactgctattttttttttcatgatttatatcatgcattcatatttaaatacttcaatctgagcacacctgttttggctttacagCGGTTATCAGCAGATGCTGCTTTGCAGCATGAGTGGTTCCGTGAAGTTCCTCTACCTAAATCAAAGGATTTCATGCCAACATTCCCTGCTCTAAATGAAT

upper sequence: GRMZM2G139038_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0010g02550.t01 (Vitis vinifera), 3'ss of exon 4
-----------gtgcaacttttac-----tctcaaatcggcatttgatattctta-ttatcatc--attcgtaccagtctgagcacacttgtttctcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAAC
           || |||| | ||      | |  |       |||  | ||||   ||   ||     |  |     |         |||  |  |||  ||||| | ||  |||| || | |||||| || ||  | ||||||   ||||||||||| || ||||| ||||| |||||||| || ||||||||||   |||  |
gtgattttttagttcaacatctataaatgttttgaggaaatgttttgttttctaggttggtatttagataatgttgtttattatggcctttatgttctattacagAGGATTACAGCTGAAGCTGCTCTTAACCATGATTGGTTCCGCGAAGTTCCTCTTCCCAAATCTAAAGATTTCATGCCTACTTTTCCTGCTCAGCATGCCC
















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|67025629|gb|CO454378.1|CO454378
EST:     AAGCTGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAGgtgcaacttt ... tcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT
EST: gi|67025976|gb|CO454725.1|CO454725
EST:     AAGCTGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAGgtgcaacttt ... tcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT
EST: gi|13388885|gb|BG462452.1|BG462452
EST:     NNNNNGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAG                         CGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT
genomic: AAGCTGGTTTTGATCTATTGAATAGACTGCTAACTTATGATCCTGATAAGgtgcaacttt ... tcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttattatcatcattcgtaccagtctgagcacacttgtttctcttgtacagCGCATATCAGCAGACGATGCTCTGAAACACAAATGGTTCTCTGAAGTTCCTCTGCCTAAATCAAAAGACTTCATGCCAACATTTCCTGCTCTTAATGAAC
                                   cacttgtttctctt  CT-rich tract
     ttattatcatcatt  TA-rich tract