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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctggccaagattgtcatgcttaacctttttttttgtttcttgtttttgactcgtcaactatcctttgtacag

Basic information

species Zea mays
transcript GRMZM2G124886_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 20
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctggccaagattgtcatgcttaac---------ctttttt------tttgtttcttgtttttgactcgtcaact---atcctttgtacag
|  ||||| | || ||||||||||| |||||||||||| |||||||||||||||||||||| ||||| |||||||| |||||||||||| |||| ||||||||  | ||| || |||||| | || |  ||||          ||| ||       | | ||| || ||||    |  |||  |   || || | |||||
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTTGGAAAACTGGAAGAATGTCTTCAATTGTTAATCGAAAGgtattgccatttg-ccaagactatcctatttaatagtacaatgcttattcagaaaatgtattttttattttatggtgatcacgttatattctctatacag

upper sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 11
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctggccaagattgtcatgcttaac---------ctttttt------tttgtttcttgtttttgactcgtcaact---atcctttgtacag
|  ||||| | || ||||||||||| |||||||||||| |||||||||||||||||||||||||||| || ||||| || ||||| ||| |||| ||||||||  | ||| || |||||| | || |  ||||          ||| ||       | | ||| || ||||    |  |||  |   || || | |||||
TAACATCTATGGCTAAAGAACAAGGGAAGAACAATGTTGCTTTCCTTTGTTTCTTCATGCTAGGAAAACTTGAAGAATGCCTTCAGTTGTTAATCGAAAGgtattgccatttg-ccaagactatcctatttaatagtacaatgcttattcagaaaatatattttttattttatggtgatcacgttatattctctatacag
















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|33093602|gb|CF053596.1|CF053596
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|211291669|gb|FL235609.1|FL235609
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822105|gb|BQ048129.1|BQ048129
EST:     AAGCTGGAAGAG-GTCTTCAA-TGCTAATAG-AAG                         CAATCGTATTCCGGATGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822050|gb|BQ048074.1|BQ048074
EST:     AAAGCTGGAAGAGTGTCTTCAA-TGCTAATAGAAAG                         CAATCGTATTCCGGAAGCATGCATTGATGGCCAGATCTTATCTTCCTAGCA
genomic: AAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCA-GCATTGATGGCCAGATCTTATCTTCCTAGCA
EST: gi|19821973|gb|BQ047982.1|BQ047982
EST:     AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGTAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCA
genomic: AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGG-AAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCA
EST: gi|26455841|gb|CA827424.1|CA827424
EST:     TCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19821970|gb|BQ047979.1|BQ047979
EST:     GAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: GAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATNGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCCTAGCA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCC-TAGCA
EST: gi|19822070|gb|BQ048094.1|BQ048094
EST:     AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|19822158|gb|BQ048182.1|BQ048182
EST:     AAGAGTGTCTTCAA-TGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: AAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|32929286|gb|CF034098.1|CF034098
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|32806736|gb|CD958970.1|CD958970
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATC
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATC
EST: gi|67014399|gb|CO443148.1|CO443148
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
EST: gi|26456008|gb|CA827591.1|CA827591
EST:     TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAG                         CAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA
genomic: TTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcat ... ctttgtacagCAATCGTATTCCGGAAGCAGCATTGATGGCCAGATCTTATCTTCCTAGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCATCTGTAGCCAAAGAACAAGGAAAGAACAATGTTTCTTTCCTTTGTTTCTTCATGCTAGGAAAGCTGGAAGAGTGTCTTCAATTGCTAATAGAAAGgtagaggcatctggccaagattgtcatgcttaacctttttttttgtttcttgtttttgactcgtcaactatcctttgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA