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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttacattatctagcatacaacagcaacaaagcctctaacattatctacagaatttactgttacatatcataaccctagtatttttttcttttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCAATTATGGAGCGTGCTGATGAGAATCTCCTTCCAGCAGTTTACAAG

Basic information

species Zea mays
transcript GRMZM2G462325_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G462325_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g10820.1 (Oryza sativa), 3'ss of exon 1
--gttacattatctagcatacaacagcaacaaagcctctaacattatctacagaatttactgttacatatcat-aaccctagtatttttttcttttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCAATTATGGAGCGTGCTGATGAGAATCTCCTTCCAGCAGTTTACAAG
  |||     |  |     ||| ||   |||     ||||   |     |    |  |   || | |||  || |||| |      | ||||  |||||||||| |||| || ||  |||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||
aggttgagaaaattgaggcaca-caattacat--tttctactgtagggaaacttaccttgcgtaatatagaattaaccgtttctagtctttcccttcttgcagAGCAAAGAATATTTTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCCATTATGGAGCGTGCCGATGAGAATCTCCTTCCGGCAGTTTACAAG

upper sequence: GRMZM2G462325_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0023g01270.t01 (Vitis vinifera), 3'ss of exon 1
--gttacattatctagcatacaacagcaacaaagcctctaacattatctacagaatttactgttacatatcataaccctagtatttttttcttttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCAATTATGGAGCGTGCTGATGAGAATCTCCTTCCAGCAGTTTACAAG
   ||    |  ||  |||  |   ||            ||  ||       | ||| | |||    | |  |   | || ||| | ||   ||  || ||||||||  |||||  ||||  | ||| | |||||| | || ||||| ||||| || || |||||||| |||||||| |||||||||||||| ||||| || 
ccttttttcttccttccatttagttgctttggtaataaaaattttgctctgtgcattgattgtcttctct-gtcctcataatatctgttggctta-ttacagAACAAGAAAGATTTTTGGGATTTCTCTCTCTCTCTTTCTTATCAACCTGGCCTCTATAATGGAGCGAGCTGATGAAAATCTCCTTCCAGCTGTTTATAAA
















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|76021646|gb|DT948816.1|DT948816
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|50322809|gb|CO517935.1|CO517935
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|93283078|gb|EB675342.1|EB675342
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|50334650|gb|CO529776.1|CO529776
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|50323167|gb|CO518293.1|CO518293
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|211090441|gb|FL069861.1|FL069861
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
EST: gi|89761727|gb|DY689627.1|DY689627
EST:     AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAG                         AACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC
genomic: AGGGCGCGGTCCTCCCCCACCTCCCCGCTCACCCCGTCCTCCAGCGCAAGgtaaccccgc ... tttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacagaatttactgttacatatcataaccctagtatttttttcttttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCAATTATGGAGCGTGCTGATGAGAATCTCCTTCCAGCAGTTTACAAG
                      tcataac  putative branch site (score: 2)
                            ccctagtatttttttc  CT-rich tract
                               tagtatttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacattatctagcatacaacagcaacaaagcctctaacattatctacagaatttactgttacatatcataaccctagtatttttttcttttcttgcagAACAAACAAGATACTTGGTTTCTCTGTATCTCTCATCCTCATCAATCTGGCTTCAATTATGGAGCGTGCTGATGAGAATCTCCTTCCAGCAGTTTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT