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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtag

Basic information

species Zea mays
transcript GRMZM2G042552_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042552_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 5'ss of exon 4
CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtag
 || |||||||| ||||| |||||||||||||||||   ||| |||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||          | | ||  |   |||||||  ||    ||||||||  | |||||   |  | |  |  || || || || | || |  ||  ||||||||||
TTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGAATTCAGCAAAGAGATGACCAAGgta----------tggattatgaaatgatcac--atctcttccaaaggtttttcttgtcctgta-tgcccatactagttcttacttcctgattgctgtggtgtag

upper sequence: GRMZM2G042552_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G22950.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtac----aatgcctgctaggttgcgctgtgatcact-catactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtag---------------------
 ||||| |||||| | || || ||||| ||||| ||    |||||||| || ||  || | || || |||||||| ||||| |||||||||||||| |||||||    |||   | |    |  |  ||| ||   | | |  ||||     ||  ||   |  |||   |  |||    |   || |  || | ||||||       ||                     
TTTGTCGAAGAGCGCAGAGGTTATGAAGCTTGTTAATAATCTCATGAAGGCTCCACAGATGGCTGCAACAATGCAAGAATTTAGCAAAGAGATGACTAAGgtacctttaattgtttccttatctcattgttattgatacgtgttctctgtttgatgattcagagttatgatcactgcttaacagttagtatctttgtttataatcctgagtgtattctttgatatgtgcag

upper sequence: GRMZM2G042552_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S104_29V6.1 (Physcomitrella patens), 5'ss of exon 4
CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcctgc-----taggttgcgctgtgatcactcatactctccaaaggactatcttg--cattaaactag-ctgtagtaatttttgcctcgtcgttt-atgtggtgtag----------------------------------------------------------------------
  ||   || ||||||||||| ||||||||||| |||  |||||||||||| || || || |||||||| ||||| ||| |    ||||||||||  ||||||   |  |         |  |||      ||        | ||       | |    |||  ||  |   |   | | |  || | ||  ||  || | | | |   ||                                                                         
ACTGCAGAAAAGCACTGAAGTTATGAAACTTGTAAACAACCTCATGAAAGCTCCTGAAGTGGCAGCCACCATGCAAGAACTATCTAAAGAGATGATGAAGgtatcttttccagatgtgcaatttgtatatagagtggcttcaatcctggttcgtccgctttggtcacgagttttctccgcaaaaaatattttcttctcatctcaagctttgcgagtcacttttaatcatcacagttaaatcatgtgggggttctgagattgctgtgcatggacatttgcaacag

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|113703876|gb|EE681380.1|EE681380
EST:     CCCCGGAGGTTGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|76931368|gb|DV172713.1|DV172713
EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|14255660|gb|BG878568.1|BG878568
EST:     CCCCCGAGGTCGCAGCCTCAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|4646886|gb|AI621961.1|AI621961
EST:     AGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: AGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|21759932|gb|BQ635473.1|BQ635473
EST:     AGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: AGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|44901356|gb|CK827901.1|CK827901
EST:     CCCCGGAGGTTGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACTCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|149039514|gb|EE046657.2|EE046657
EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
EST: gi|14311555|gb|BG901310.1|BG901310
EST:     CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAG                         GCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC
genomic: CCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcc ... tgtggtgtagGCTGGTGTGATGGAAGAAATGGTCAACGATGCTTTAGATTCAACGCTGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGAATTCAGCAAAGAGATGACAAAGgtacaatgcctgctaggttgcgctgtgatcactcatactctccaaaggactatcttgcattaaactagctgtagtaatttttgcctcgtcgtttatgtggtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG