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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGAATTTGGAGGTTATCTACTTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgtgcagatattgttacagagtctggtcatatgcctttgtgtaaaattgccatttattagaacctttcaaattttctgaagtattcagattgatgaaaaaatatcccagtgcattcttcatgtgccattatatatagtgtaacactttaatccactaacctttttattggtatgcttcatctgcag

Basic information

species Zea mays
transcript GRMZM2G020721_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020721_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 5'ss of exon 5
ATCTGAATTTGGAGGTTATCTACTTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgtgcagatatt-gttacagagtctggtcatatgcctttgtgtaaaattgccatt-tattagaacctttcaaa-----ttttctgaa-gtattcagattgatgaaaaaatatccc----agtgcattcttcatgtgccattatatatagtgtaacactttaatccactaacctttttattggtatgcttcatctgcag
|||||| ||||||||| |||| ||||| ||||||||||||||||| |||||  | || ||||||||||| ||||| || ||     ||| ||  ||||| || ||| |   | |  ||       | |||| |   ||||  | |   |  |      ||||  |||   ||||  |    |   || || ||      ||||| |   | ||||||  || | |  | ||  ||| |||  |   || |||||||   || ||| ||  ||||||||
ATCTGAGTTTGGAGGTCATCTGCTTTACTTTTACATATGTGATCGCACAAATCTACTGGGAGAGTCTGCGAAGgtgctattacattgatgtttattaca-agcctgatttcacgt-ttgaaaagtagttgcaaaaatattgtatctagttgagatatcttttacgaatacattctaagccttactaatatttcatggaaagtgcctatataatgtgctgttcttt-caatgggacattttt-tgttctgaccttttc--tgttatcctgtatctgcag
















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|148982690|gb|EE028501.2|EE028501
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
EST: gi|148986950|gb|EE030765.2|EE030765
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
EST: gi|71448158|gb|DR829208.1|DR829208
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
EST: gi|211035508|gb|FL319750.1|FL319750
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
EST: gi|211342552|gb|FL342004.1|FL342004
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATC
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATC
EST: gi|91875375|gb|EB405332.1|EB405332
EST:     TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAG                         AATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
genomic: TTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA
EST: gi|211440830|gb|FL365412.1|FL365412
EST:     TTATTTTTACATATGTGATCGTAACAA-CTTGCTTGGAGAGTCTGC-AAG                         AATTACAGCCGAGATCTGTTCCTTTCCCTCTACTTTCTTCTTATCATTGGA
genomic: TTATTTTTACATATGTGATCGTA-CAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgt ... tcatctgcagAATTACAGCCGAGATCTGTTCCTTTTCCTCTACTTTCTTCTTATCATTGTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGAATTTGGAGGTTATCTACTTTATTTTTACATATGTGATCGTACAAACTTGCTTGGAGAGTCTGCCAAGgtactgttgtgcagatattgttacagagtctggtcatatgcctttgtgtaaaattgccatttattagaacctttcaaattttctgaagtattcagattgatgaaaaaatatcccagtgcattcttcatgtgccattatatatagtgtaacactttaatccactaacctttttattggtatgcttcatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA