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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT

Basic information

species Zea mays
transcript GRMZM2G124919_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 3
gtttgtattcatcatgtacctgacatttccaaaatagtttg-acagta-------ttttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT
|||  |  | ||| | | | ||    || ||||||  | |  | ||||       || |||||  ||||| ||   || ||| |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||| | |  || || ||||| 
gttcctgatgatcgtattcttgtttgttgcaaaatcatatacatagtacatctacttatctgaactttgtatg--attctttcttcagAGGTATGTTTAATAAAGAAAGAATTGCAAAGATGAAGAAAGGTGTAATCATTGTGAATAATGCTCGAGGAGCAATCATGGATACCCAGGCGGTTGCAGAC

upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 3
----gtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattt------------tctgagtttt--gtttgctgttttttt--ttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT
      ||  ||  | ||| | | |||   |  ||    | ||  |||  ||||             || | || |  |  |  || | || |  |||||||| ||||| ||||||||||||||||||||| |||| || || ||  |  |||| || |||||||||||||||||||||||| | | ||| || || |||
gccccctttcatataccatttgcttgaatctagcatggcaattctacaaaatttgtgttgttgaaccctaaattatcagaattttgatcttgtaattcagAGGAATGTTCAACAAAGAGAGGATTGCAAAGTTGAAAAAGGGAGTTCTAATTGTTAACAATGCTCGAGGAGCAATCATGGATACACAAGCTGTTGCCGAT
















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|31354982|gb|CD439339.1|CD439339
EST:     CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAG                         AGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
genomic: CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattc ... tttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
EST: gi|32849118|gb|CD988799.1|CD988799
EST:     CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAG                         AGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
genomic: CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattc ... tttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
EST: gi|32916182|gb|CF020994.1|CF020994
EST:     CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAG                         AGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
genomic: CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattc ... tttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
EST: gi|32863793|gb|CF003475.1|CF003475
EST:     CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAG                         AGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
genomic: CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattc ... tttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGT
EST: gi|78026309|gb|DV494696.1|DV494696
EST:     CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAG                         AGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGT
genomic: CCAAAGTGTGATGTGATTGTGATCAACACACCTCTTACGGAGAAAACAAGgtttgtattc ... tttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaaaatagtttgacagtattttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT
           gtttgac  putative branch site (score: 4)
                               ttttgtttgctgtttt  putative PPT
                                         tgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtattcatcatgtacctgacatttccaaaatagtttgacagtattttctgagttttgtttgctgtttttttttcagAGGCATGTTTAACAAAGAGAGGATTGCAAAGATGAAGAAAGGTGTAATTGTTGTGAATAATGCTCGAGGAGCAATCATGGATGCTCGAGCAGTCGCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT