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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcgttgcagccataagatgtgctctctttttttcaaactaacaaggcattaatgagattcatgaaccgattgtgctgctattgaatttatttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTG

Basic information

species Zea mays
transcript GRMZM2G086052_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 3
agcgttgcagccataagatgtgctctctttttttcaaactaacaaggcattaatgagattcatgaaccgatt-gtgctgctattga-atttatttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTG
  |   |||    |    ||||     | |    |||   |   | |  ||  ||  ||         |||  | ||   || |||  ||| |||  | ||||||| |||||| |||||||||||||||||||||||||||||  |||||| ||| || ||||||||||||||||| ||||| || ||||| |||||||| |
-tcaaagcaattcttct-tgtgaagattataggacaattaattcatgtgttcgtgctatggggtgctagatgagagcaattaatgatgtttcttttcctcagATGACTGGTGTGTGGGCAATGTGCCTCTGGGAGCAAATGGGGCAGCCAGAGAAAGTCAATCTGATTGAGCTTGGTCCAGGGCGCGGAACTCTCTTGGCAG

upper sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G28700.2 (Arabidopsis thaliana), 3'ss of exon 3
agcgttgcagccataagatgtgctctctttttttcaaactaacaaggcattaatgagattcatgaacc---gattg---tgctgctattgaatttatttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTG
   ||      | |    | || |   ||       |   |     |  ||  |   ||   ||| |    |||||   |  || || |   | |  |   |  ||||||||||||| ||| |  |||| || |||||||||||||||| ||||| || ||| |||||  ||||||| || ||||| || ||||||||| |||| |
---gtgatttacttggcgtttgttgatttgagagttatgcatttgtgttttggttctatgtttgagcttgagattgaagttttgttactttgtgttgtgatcttagATGATTGGTGTTTGGACCGTGTGTCTTTGGGAGCAAATGGGAAGGCCAGAGAGGGTTAATCTTGTTGAGCTAGGTCCAGGTCGGGGAACACTCATGGCCG
















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|71326245|gb|DR799816.1|DR799816
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|32792113|gb|CD944349.1|CD944349
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|32826797|gb|CD966475.1|CD966475
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTCGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|93016466|gb|EB641986.1|EB641986
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTCTGGAGAG                         ATGATTGGTGTATGGGCAATGT
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGT
EST: gi|71297897|gb|DR784919.1|DR784919
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|93281358|gb|EB673622.1|EB673622
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|78108018|gb|DV526436.1|DV526436
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|71313522|gb|DR793329.1|DR793329
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|71297664|gb|DR784782.1|DR784782
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|149097668|gb|EE183570.2|EE183570
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|93281137|gb|EB673401.1|EB673401
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|76293021|gb|DV032589.1|DV032589
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|32824168|gb|CD963890.1|CD963890
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|78090509|gb|DV518883.1|DV518883
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
EST: gi|89251237|gb|DY623023.1|DY623023
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTC
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTC
EST: gi|71772608|gb|DR970536.1|DR970536
EST:     AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAG                         ATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG
genomic: AATCAGGGGATTTCATCACCTCGCCAGAGGTCAGCCAGATGTTTGGAGAGgtaaaactgg ... tttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcattaatgagattcatgaaccgattgtgctgctattgaatttatttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTG
  cattaat  putative branch site (score: 3)
                                         tttattt  putative PPT
                                  tattgaatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcgttgcagccataagatgtgctctctttttttcaaactaacaaggcattaatgagattcatgaaccgattgtgctgctattgaatttatttggcacagATGATTGGTGTATGGGCAATGTGCCTCTGGGAGCAAATGGGAAAGCCAGCGAAGGTGAATCTGATTGAGCTTGGCCCAGGACGAGGAACACTCTTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT