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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga...

Basic information

species Zea mays
transcript GRMZM2G080930_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 5'ss of exon 2
AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt-ttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga
| |||||| | ||||||||| |||||||||||||||||||| | || |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||| ||| |    |  |  | ||     ||  | ||  |   | |  | |||||| |||  ||   |   || ||||  |  ||      |  ||||   
ATTTGTTCACGATGGCCCGCTTGTATGTTGGCAACTTGGATCCCCGAGTGACTTCCGGGGAACTTGAAGATGAGTTTCGTGTGTTTGGAGTTCTGCGAAGgtcagtttctgcctaggcaatttttccacttcatctaattgggtgtt-tggtttttgcattgtgctgcattagtcttgtgtagtttttggatagactagtt

upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G17930.4 (Glycine max), 5'ss of exon 2
AATTGTTCTCA-ATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttt-----ttttcaaactttat----tcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattg-gcaagttaactaaga
  || |    | ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| | || |||| | ||       ||| | | ||||     |||  ||   | | ||||| | |  |  | | ||   ||||  |   ||   |||  || ||  ||   ||        
-CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaacacgctttaatattttaccctctcaatttcgttgtggatacttctatttctctgttttggttg--ctatgatttttgtttggttttgctgatt--------

upper sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G29080.2 (Glycine max), 5'ss of exon 2
AATTGTTCTCA-ATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga----
  || |    | ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || ||||| || || |||||| | || |||| | ||   |     ||||| |    |||  | |  ||    ||  | | |  ||||  || |   |   |  |  | |||||      ||   |  |     
-CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaactc---gctttaatattatttcctctcaatttcgttt-tggatacttcaatttctaagttttggttgcagtgatttttttttttgtttggctgtt

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|211274557|gb|FL349470.1|FL349470
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211470387|gb|FL342153.1|FL342153
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211047373|gb|FL359874.1|FL359874
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTRTTGATTTTKACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211158830|gb|FL334283.1|FL334283
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211205317|gb|FL316783.1|FL316783
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211416748|gb|FL321413.1|FL321413
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211310251|gb|FL338861.1|FL338861
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211055147|gb|FL320204.1|FL320204
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211072623|gb|FL332514.1|FL332514
EST:     ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
EST: gi|211091140|gb|FL328973.1|FL328973
EST:     ACTTCTGGGGAACTCGAACATGAGTTCCGTGTGTTTGGAGTTCTGCGAAG                         TGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA
genomic: ACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttttt ... ctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGTTCTCAATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcactttttttcaaactttattcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattggcaagttaactaaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG