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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

Basic information

species Zea mays
transcript GRMZM2G408989_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
gtaagt-tgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
|||||    |  |  | ||||| |   || |  |||||||  |  | | |  |||  |  || |  | | | ||| |||||| |||||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgttctatatatgaaaagaagttc--tgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG

upper sequence: GRMZM2G408989_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 4
-----gtaagttgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccacta-atggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
       | | ||  | |      |  | |    || |||  |||     ||  ||  | | ||| |  ||| || || |   | || |||| ||     | ||| | || || |||||| |||||||||||||||| |||||||||||| | ||
gtaataaaggctgaaaataagaactactttgaaattatatgtcaa---ccttagcaata-tcctgacttctatattgttttactattacagCCTGTGCCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTATTTCATCAG
















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|18169894|gb|BM339734.1|BM339734
EST:     CACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: CACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|16920990|gb|BM074929.1|BM074929
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|6022165|gb|AW067093.1|AW067093
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|32835284|gb|CD974962.1|CD974962
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|78080743|gb|DV509155.1|DV509155
EST:     GTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: GTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211107178|gb|FL251311.1|FL251311
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTACCGTTATTTCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|18169973|gb|BM339813.1|BM339813
EST:     TCACGGAGGGTCATCACAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: TCACGGAGGGTCATCACAGCAGATGGATCCgtaagttgtc ... tttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
                                cactaat  putative branch site (score: 2)
                                         tctatttctttc  putative PPT
        aaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcacttttgtatggtatagtgttttatcccaaatgttttctcagaactgctgtccactaatggtctatttctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT