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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaatttactgtttctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 10
-tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaatttactgtttctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG
  |||    | |   |    |        | | | | | |    |     |||    ||| |  |      ||||      |  || |||    ||| |||||||||||||| || || ||||| || ||||||||||| ||||| |||||||| ||||||||||||
accaccacatgcatctttctggctggcttagtcagcctatgaaagcca-tatactggattcacatatcttataatacctcctaactattttcacttggcagATATTTTACTTTGTCGGGTTTGGATTATTCTGCCTTGAGTCACTGCTGAGCATTGGTGTCATTCAG

upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaattt---actgttt-ctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG
     ||| || |||       |      ||  |  ||  ||  ||    |    |  ||  ||   |      ||   |   ||| |  ||  | | |  |||||||| ||| |  |||||||||| |||||||||||||||||||| || || ||| | ||  |||||
----ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG
















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|31353834|gb|CD438191.1|CD438191
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|149104176|gb|EE289610.2|EE289610
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|71322126|gb|DR797758.1|DR797758
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|211044188|gb|FL461688.1|FL461688
EST:     TGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|37400724|gb|CF637721.1|CF637721
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|113702575|gb|EE680079.1|EE680079
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCATGAATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|78112245|gb|DV530639.1|DV530639
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|78180134|gb|DV550507.1|DV550507
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|76927276|gb|DV171212.1|DV171212
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|5847119|gb|AW000198.1|AW000198
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGGTCTGCCTTGGATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|15082749|gb|BI389433.1|BI389433
EST:     ATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: ATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|60396504|gb|DN229373.1|DN229373
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTC
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCC
EST: gi|32851209|gb|CD990890.1|CD990890
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|37374257|gb|CF623473.1|CF623473
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|78081464|gb|DV509876.1|DV509876
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|76289052|gb|DV028620.1|DV028620
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|5343187|gb|AI795372.1|AI795372
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTTGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|91876330|gb|EB406287.1|EB406287
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
EST: gi|8551590|gb|BE128935.1|BE128935
EST:     TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGG                         ATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC
genomic: TGGGATTTTACCAGCAATTGATGTCATAAGCAAGAATGCTATTGTCGGGgtaagtctgt ... tgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcatagcttatttagttcctaagtaatttactgtttctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG
                                   tttctttttatgttt  CT-rich tract
                         taatttactgtttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcactctttaccaatcgacgctacatccaataatcatgtattggttggcatagcttatttagttcctaagtaatttactgtttctttttatgtttgacagATATTTTACTTCGTTGGATTTGGCTTGTTCTGCCTTGAATCACTTCTGAGCATCGGTGTCATTCAG

- - - - - - - - - - ctacatc
- - - - - - - - - - - - - - - - - catgtat