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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtacctaagtttttgaattttctctatgccacattcttacctttctctatgataagtgctaaacagatacctgcatgaaaacttttcag

Basic information

species Zea mays
transcript GRMZM5G850355_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 5'ss of exon 3
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgta-cctaagtttt-----tgaatt--ttctcta------tgccacattcttacc----tttctctatgataagtgctaaacagatacctgcatgaaaacttttcag
|||| || |||||||| || ||||| ||||||||| |||||||||||||||| ||||||||||||||| || || | | | | ||     ||||||  |  | ||      ||| |||| ||   |    ||| | | | | |||  ||||  | |||  |  ||| |||   |||||
CTGCTAATGGTGTAGTTATCGCCACTGAGAAGAAATTGCCTTCTATTTTAGTCGATGAAACATCTgtaagtctaacatcactcttaatgctgaattcctcttttagtgagttgcgacatgctattcgttgtttgtttctcagaagcactaa-tacatagttatatgcaaa---ttcag

upper sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G25940.3 (Glycine max), 5'ss of exon 4
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtacctaa-gtttttgaatt-ttctctatgccacattcttacctttctctatgataagtgctaaacagatacctgcatgaaaacttttcag-----
|||| || || || || |||||||||||||||||| |||| ||||| || || ||||||||||| ||  || ||  |   ||| ||  ||  || | | | |   |||| |   | |  |  || | | ||   ||  | |   ||  |   |      ||      
CTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCAgtgagtttattttccgttattagatccttttttgttcattattcatgt-tataacagtgtttactgtgtaat-gttgtgtgtcttggatgcccacactaagc

upper sequence: GRMZM5G850355_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 5'ss of exon 3
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac------ctaagtttttga-attttctctatgccacattcttacctttctctatgataagtgct-aaacagatacctgcatgaaaacttttcag
||||||| ||||| || ||||| || ||||||||||| |||||||| || ||||||||  |||| ||  ||  |       ||||||||||||   ||| | |||      |||| || |||       |||| |  |   |   ||  |  | |   |  |  |   
CTGCCAATGGTGTTGTTATTGCAACTGAGAAGAAACTACCTTCTATCTTGGTGGATGAGGCATCGgtgagtcaattgtggactaagtttttgatgatttgtatatttttttttctcactttttctgggtataactttttggatgaatggcgtcctagcacttcat---

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|60346286|gb|DN213259.1|DN213259
EST:     TGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATAGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|6020544|gb|AW065472.1|AW065472
EST:     GCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: GCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|14203539|gb|BG837216.1|BG837216
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|15427202|gb|BI543024.1|BI543024
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|32934694|gb|CF039506.1|CF039506
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211017640|gb|FL189740.1|FL189740
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|22520740|gb|BU079551.1|BU079551
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|5566889|gb|AI881800.1|AI881800
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|87156656|gb|DY401445.1|DY401445
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|14242859|gb|BG840665.2|BG840665
EST:     TGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|113702959|gb|EE680463.1|EE680463
EST:     GTGGATGAAACATCT                         G-GCAAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTTTATAG
genomic: GTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGC-AAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211014870|gb|FL189739.1|FL189739
EST:     TTGCCACCGAGAAAGAAACTGCCTTCCTATTTTAGTGGATGAAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAAATATTGGAGTTGTCTATAG
genomic: TTGCCACCGAGAA-GAAACTGCCTTC-TATTTTAGTGGATGAAA-CATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAA-TATTGGAGTTGTCTATAG
EST: gi|211535545|gb|FL366410.1|FL366410
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|32908069|gb|CF012882.1|CF012882
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|9254141|gb|BE344609.1|BE344609
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211408164|gb|FL390201.1|FL390201
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAATATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|9461620|gb|BE453822.1|BE453822
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211156517|gb|FL164231.1|FL164231
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|14204267|gb|BG837944.1|BG837944
EST:     TGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|5456374|gb|AI834064.1|AI834064
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|29167732|gb|CB410992.1|CB410992
EST:     TGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|8367928|gb|BE050873.1|BE050873
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|12967998|gb|BG264945.1|BG264945
EST:     TGATTGCCACTGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211158124|gb|FL164253.1|FL164253
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGCAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211370171|gb|FL333604.1|FL333604
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|32912475|gb|CF017287.1|CF017287
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|40337252|gb|CK371322.1|CK371322
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|67018206|gb|CO446955.1|CO446955
EST:     TGATTGCCACCGAGAAG-AACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211100498|gb|FL307608.1|FL307608
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|26559204|gb|CA831439.1|CA831439
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|211352174|gb|FL343457.1|FL343457
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|31355634|gb|CD439991.1|CD439991
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
EST: gi|32906923|gb|CF011736.1|CF011736
EST:     TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTGGTGGATGAAACATCT                         GTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG
genomic: TGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtac ... aacttttcagGTGCAAAAGATTCAGGCACTAACACCAAATATTGGAGTTGTCTATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCCAACGGTGTAGTGATTGCCACCGAGAAGAAACTGCCTTCTATTTTAGTGGATGAAACATCTgtatgtgtacctaagtttttgaattttctctatgccacattcttacctttctctatgataagtgctaaacagatacctgcatgaaaacttttcag

- - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA