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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagattcataaatcataataccaatgagatgtcctggtattatgaccatgttattacattttagatgaattcatacttcactcttgtcctttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAAATGTATTTTGATGAACTTCTTCCAAGATTGGTGAAAGAAGGAAGTGATG

Basic information

species Zea mays
transcript GRMZM2G124365_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124365_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 3'ss of exon 3
--caagattcataaatcataataccaatgagatgtcctggtattatgaccatgttattacattttagatgaattcatacttc-actcttgtcctttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAAATGTATTTTGATGAACTTCTTCCAAGATTGGTGAAAGAAGGAAGTGATG
  ||    |    | ||| | | | |||    |    || | || |     | | | || ||||      |||||||| ||    ||||||| ||| |   ||||||||||||| |||||||||||||| ||||||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||
accatctattgagactcacattgctaattgattactgtgctgttgtattgttataagtaaatttggataaaattcatatttttgttcttgtcttttct---agGTTTTGCATCCTATTGCTGATTCTATTAATATCAACAAGGAGATTTGGAAAATGTATTTTGATGAGCTTCTTCCAAGATTAGTGAAAGAAGGAAGTGATG

upper sequence: GRMZM2G124365_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G06660.1 (Glycine max), 3'ss of exon 2
caagattcataaatcataataccaatgagatgtcctg-gtattatgaccatgttattacattttagatgaattcatacttcactcttgtcctttgtcata---gGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAAATGTATTTTGATGAACTTCTTCCAAGATTGGTGAAAGAAGGAAGTGATG
 ||| || | | |  ||  |     |    |  | |  |  || |     ||  |||| ||||| ||  |||  |   |  | | ||     |  | |||   |||| |||||| |  |||||||||||||||||| |||||  |||||||||| ||||||||  | || || |||||||||||||| ||||  |||  |||||
-aagtttaaaagaaaattgtgttccttttttagcttatgcgttgtatttctg--attatatttt-gactaatctaccttcaattgttccttgtaattatactagGTTCTGCATCACTGTGCTGATTCTATCAATATAAACAATAAGATTTGGAATATGTATTTGAAGGATCTCCTTCCAAGATTGGTAAAAGCGGGAGATGATG
















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|32842677|gb|CD982358.1|CD982358
EST:     CAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: CAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32842515|gb|CD982196.1|CD982196
EST:     ACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: ACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|149077331|gb|EE166010.2|EE166010
EST:     CCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: CCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32842440|gb|CD982121.1|CD982121
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|149071764|gb|EE160157.2|EE160157
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|211304786|gb|FL143335.1|FL143335
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32851768|gb|CD991449.1|CD991449
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|211304784|gb|FL143333.1|FL143333
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32842684|gb|CD982365.1|CD982365
EST:     NTTCCAAGGATCTGCCTGAGCNCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32851767|gb|CD991448.1|CD991448
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|67010340|gb|CO439089.1|CO439089
EST:     CCCCGGTTGCCACCTATGCAATACCCAA-G                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: CCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
EST: gi|32842553|gb|CD982234.1|CD982234
EST:     TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACTCAAGG                         GTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA
genomic: TTTCCAAGGATCTGCCTGAGCCCCGGTTGCCACCTATGCAATACCCAAGGgtaatgcatg ... tttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatgttattacattttagatgaattcatacttcactcttgtcctttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAAATGTATTTTGATGAACTTCTTCCAAGATTGGTGAAAGAAGGAAGTGATG
                               cttcactcttgtcctt  CT-rich tract
      ttattacattttagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagattcataaatcataataccaatgagatgtcctggtattatgaccatgttattacattttagatgaattcatacttcactcttgtcctttgtcatagGTTTTGCATCCCATTGCTGATTCTATCAATATCAACAAAGAGATTTGGAAAATGTATTTTGATGAACTTCTTCCAAGATTGGTGAAAGAAGGAAGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA