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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattcaatctttaactagtgtacagattttgaatggtatcccttttcatgtactgaactgtgtttaatgggcatttgaccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAATTTGGAATCAAAGAAATTTGCAGGACAGGAAAA

Basic information

species Zea mays
transcript GRMZM2G407044_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 4
gtaaaattcaatctttaactagtgtacagattttgaatggtatcccttttcatg--tactgaactgtgtttaatgggcatttgaccaa-tgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAATTTGGAATCAAAGAAATTTGCAGGACAGGAAAA
               |||  ||  | | ||||   |  ||| | | |    |||  |   | | |   ||| ||| | |||||| ||| |  |||||| ||||||||||||||||||||| ||| ||||| ||||| ||  | |||||||| || ||||||||||| || || ||||||
--------------gtaa--agactcctgattccaacaggtttacatacatatgattgtaggaattcctttgatgtgtatttgatcaagttgtagGTAACTGGAGATCCTGGCAAAATTGTTGCTGTGCAAAGGAACCTCAGCAAATTTGGGATAAAAGAAATTTGTAGAACGGGAAAA
















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|148959834|gb|EE153063.2|EE153063
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|149075260|gb|EE163764.2|EE163764
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|149087824|gb|EE177122.2|EE177122
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|33098451|gb|CF058411.1|CF058411
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAGTCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|78122764|gb|DV541148.1|DV541148
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAAAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|71435773|gb|DR816823.1|DR816823
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
EST: gi|148949305|gb|EC894756.2|EC894756
EST:     TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAG                         GTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA
genomic: TTTTCAGAGCAAAAGTTGTTGATATATCTGAGAAAACACTTACCATGGAGgtaaaattca ... ccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatcccttttcatgtactgaactgtgtttaatgggcatttgaccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAATTTGGAATCAAAGAAATTTGCAGGACAGGAAAA
                                       atttgac  putative branch site (score: 4)
                           tgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattcaatctttaactagtgtacagattttgaatggtatcccttttcatgtactgaactgtgtttaatgggcatttgaccaatgctagGTAGCTGGAGATCCTGGCAAAATTGCTGCAGTGCAGAGGAATCTATGGAAATTTGGAATCAAAGAAATTTGCAGGACAGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA