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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctggattgaattgaagcatttggtcttagtaagattgaagaaaaaggaataaatttgcatattcttgtgatgagttatgctctgttatcctcatt...

Basic information

species Zea mays
transcript GRMZM2G171745_T05
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 7
TCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctggattgaattgaagcatttggtcttagtaagattgaagaaaaaggaataa--atttgcatattcttgtgatgagttatgctctgttatcctcatt
|||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| || |||||||  || ||||| ||||||||||||||||||||||| |||||  | ||||||||     | |     || ||     | |  |||| |  |   | | |        |  |  |    |||||| |  |    
TCAGGAGAAAATTAAGTGGGCTGATACAATGAGTGAAGTGAACAAGAAGCACCAGAAAGAGTTCGAAGACAAGGTAGAAGAAGCCAAAAAATCAATCAAGgtgagttggatcaatttgaagcaccaactatactgtagtttttcagatattgaatgatgaacagtaaaaaaggaaaaaaaacttgcatctgttttgtttt--
















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|37419216|gb|CF647286.1|CF647286
EST:     CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCNNNNNNNTCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCC-AAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|149027222|gb|EE046433.2|EE046433
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|60398630|gb|DN231446.1|DN231446
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|78109059|gb|DV527476.1|DV527476
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|113702753|gb|EE680257.1|EE680257
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|211477594|gb|FL101253.1|FL101253
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGGAGAAAATCAAGTGGGCTGACACAATGAGTGAGGTGAACAAGAAGCACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctggattgaattgaagcatttggtcttagtaagattgaagaaaaaggaataaatttgcatattcttgtgatgagttatgctctgttatcctcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG