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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaggctacaaattttactttgttatgctattggtttgtgctttgacctttgatacattattaagcctgaatttgcattctttgatttatgaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG

Basic information

species Zea mays
transcript GRMZM5G825902_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 6
ttaggctacaaattttactttgttatgctattggtttgtgctttgacctttgatacatta--ttaagcctgaatttgcattctttgatttatgaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG
    |  | ||| ||   ||  | |   | ||| | ||   ||     | |  | |||||  || ||| ||||  ||  || |||| | | | ||||   |||| ||||||||| ||| ||||||| || ||||||||||||| ||||| ||||||||
--cagtaaaaaagttaggttcctgagtgttttgttatgctgttaattttgtattccattaactttagcatgaacgtgatttatttgttctttaaactctcagGTTGATGTTGATGTTGTAACACATGTAATTGTTGAAGATGATGGACCTAAAAGAAG
















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|211056798|gb|FL037810.1|FL037810
EST:     AATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|60394392|gb|DN227262.1|DN227262
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|116828950|gb|EC862572.1|EC862572
EST:     GAAGTTAGCCATGGGTGAATTTTTTGTGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: GAAGTTAGCCATGGGTGAATTTTTTG-GGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|60394317|gb|DN227187.1|DN227187
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|71762075|gb|DR960012.1|DR960012
EST:     AGAAGTTAGGCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|24934311|gb|CA452529.1|CA452529
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31356321|gb|CD440678.1|CD440678
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGGTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31353042|gb|CD437399.1|CD437399
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|6194493|gb|AW146597.1|AW146597
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|194716957|gb|FK934116.1|FK934116
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTCGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|31360452|gb|CD444809.1|CD444809
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|149074677|gb|EE163095.2|EE163095
EST:     AAGTTAGCCATGGGGGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|32828950|gb|CD968628.1|CD968628
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
EST: gi|32828741|gb|CD968419.1|CD968419
EST:     AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAG                         GTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA
genomic: AGAAGTTAGCCATGGGTGAATTTTTTGGGATAAAACCTCCTGAGAAGAAGgcaagtgcaa ... gaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttgatacattattaagcctgaatttgcattctttgatttatgaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG
     tgatacattattaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaggctacaaattttactttgttatgctattggtttgtgctttgacctttgatacattattaagcctgaatttgcattctttgatttatgaactggtagGTAGATGTTGATATTGCAACACATATAGTTGTTGAAGATGACGGACCAAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG