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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtaacattgatatattttggtttttttttttgaaaaatagaaagaaagagcattatctggcaactgatttgtttactttgcttttttgtcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTG

Basic information

species Zea mays
transcript GRMZM2G324540_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 3
---ttgtaacattgatatattttggtttttttttttgaaaaatagaaagaaagagcattatctggcaa-ctgatttgtttactttgcttttttgtcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTG
   || |||        | |||| |||     |||||     |   |||||    |||||||  | || ||||| |||||| ||   || | |  |  ||||||||||| |||||||||||||||||||| ||||||||||| ||| ||||||| || |||||||||||||||||||||||||||||||||||||| ||  | |
ccgttttaatgaaatgctcttttagttaacacttttgc----ttttaagaacattcattatcctgtaatctgatctgtttagttgttttatgtcccttttccagCATGATGCTGCCTGCCGTGTTATAGCTAGATTAAAGAAAGAACGAGATGAAGCCAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCATCGATGG
















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|211270237|gb|FL344649.1|FL344649
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCNCTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211156212|gb|FL365662.1|FL365662
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211089285|gb|FL354017.1|FL354017
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGNGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211206059|gb|FL353696.1|FL353696
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGGACGCTGCCTGCCGTGTTATAGCCCAGATTAAAGAAAGGAAAGAGAT
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATG-ACGCTGCCTGCCGTGTTATAGCC-AGATTAAAGAA-GGAAAGAGAT
EST: gi|211228973|gb|FL343790.1|FL343790
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211040670|gb|FL334591.1|FL334591
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211158673|gb|FL319015.1|FL319015
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211165501|gb|FL341377.1|FL341377
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211227097|gb|FL350438.1|FL350438
EST:     AGCAGCAGCTTCACACAGCAAGACNAGAACTTAGTCATGCACTCTACCAG                         CATGGACGCTGGCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGA
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATG-ACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGA
EST: gi|211108070|gb|FL361613.1|FL361613
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAAGGAA-GAGATGA
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAA-GGAAAGAGATGA
EST: gi|211444525|gb|FL325223.1|FL325223
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211050070|gb|FL348912.1|FL348912
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGGCGTGGTTATTGCCCGATTTAGGAAAGGAAAGA
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTG-TTATAGCCAGATTAAAGAA-GGAAAGA
EST: gi|9254345|gb|BE344813.1|BE344813
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211367120|gb|FL319134.1|FL319134
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGANAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211096168|gb|FL332998.1|FL332998
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211262919|gb|FL344603.1|FL344603
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTNGCCTGCCGTGTTATAGCCAGATTAAAGAAG
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCT-GCCTGCCGTGTTATAGCCAGATTAAAGAAG
EST: gi|211162340|gb|FL348127.1|FL348127
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGGCCGTGT-ATAGCCAGATTAA-GAAGGAAAGAGATGA
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTG-CCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGA
EST: gi|211411809|gb|FL328773.1|FL328773
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211170529|gb|FL341423.1|FL341423
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGGCCGTGGTATAGCCAGATTAAAGAAAGGAAAGAGAAT
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTG-CCGTGTTATAGCCAGATTAAAGAA-GGAAAGAGA-T
EST: gi|211306361|gb|FL348172.1|FL348172
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211314342|gb|FL341215.1|FL341215
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGGCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|148945896|gb|EC891188.2|EC891188
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|67020062|gb|CO448811.1|CO448811
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGAC
EST: gi|211108071|gb|FL361614.1|FL361614
EST:     AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAG                         CATGACGCTGNCCTGCCGTGGTATAGNCAGATTAAAGAAAGAAAGAGATGA
genomic: AGCAGCAGCTTCACACAGCAAGACAAGAACTTAGTCATGCACTCTACCAGgtcttccatt ... tcccttccagCATGACGCTG-CCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagagcattatctggcaactgatttgtttactttgcttttttgtcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTG
                  aactgat  putative branch site (score: 3)
                        tttgtttactttgctt  CT-rich tract
                       atttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtaacattgatatattttggtttttttttttgaaaaatagaaagaaagagcattatctggcaactgatttgtttactttgcttttttgtcccttccagCATGACGCTGCCTGCCGTGTTATAGCCAGATTAAAGAAGGAAAGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA