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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagtgcacgatttgttgtttgattgtggcatcatactgctgctataaaaatgatgcttgaaaactaaatctactggctgcctcttgtccttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAATAGCAGCTTAGCCATCAATCCTCGCTACGTCCGGTCCTGGTTGGATCTTT

Basic information

species Zea mays
transcript GRMZM2G451366_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 10
tacagtgcacgatttgttgtttgattgtggcatcatactgctgctataaaaatgatgcttgaaaactaaatctactggctgcct----cttgtccttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAATAGCAGCTTAGCCATCAATCCTCGCTACGTCCGGTCCTGGTTGGATCTTT
||      | ||||  | |  ||||  |           | |||        ||    |   ||   || |  ||  | |        ||  | |   ||||||||||||||||||||| | | ||| | |||||| ||||||||||| ||||| ||||| ||||||||||| |||| |||| ||| |||||||||||||||||
tagctactatgattaat-gagtgatattaaagctgactagttgcctctt---tgcctttctgaactgaagttgaccagttcttatatactaattccatttacagAGACACATCTATGGACTAAAAGGAAAGAATATTGATGTTTTTGCGGAGAACAGCAGTTTAGCCATCAACCCTCACTACATCCAGTCCTGGTTGGATCTTT
















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|32847269|gb|CD986950.1|CD986950
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32841613|gb|CD981294.1|CD981294
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32840746|gb|CD980427.1|CD980427
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32841252|gb|CD980933.1|CD980933
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32839985|gb|CD979666.1|CD979666
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32839499|gb|CD979180.1|CD979180
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGGATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32839696|gb|CD979377.1|CD979377
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32840986|gb|CD980667.1|CD980667
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32841145|gb|CD980826.1|CD980826
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32840104|gb|CD979785.1|CD979785
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32840762|gb|CD980443.1|CD980443
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|89252033|gb|DY623819.1|DY623819
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32863734|gb|CF003416.1|CF003416
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32841116|gb|CD980797.1|CD980797
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32841526|gb|CD981207.1|CD981207
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
EST: gi|32945502|gb|CF050321.1|CF050321
EST:     ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCG                         AGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT
genomic: ATGTTGAGTCAGTAATCCGAACTGTCAGATTAGTTTCTGAGAGTCTTGCGgtaagttaaa ... cttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaaaatgatgcttgaaaactaaatctactggctgcctcttgtccttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAATAGCAGCTTAGCCATCAATCCTCGCTACGTCCGGTCCTGGTTGGATCTTT
                  aactaaa  putative branch site (score: 2)
                                 ctgcctcttgtccttc  putative PPT
                aaaactaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagtgcacgatttgttgtttgattgtggcatcatactgctgctataaaaatgatgcttgaaaactaaatctactggctgcctcttgtccttcttacagAGACACATCTATGGATTGAGAGGGAGGAATATCGATGTTTTTGCAGAGAATAGCAGCTTAGCCATCAATCCTCGCTACGTCCGGTCCTGGTTGGATCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT