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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataactaaagccgaaaaattcagacaaattagtttgctagctgtgtacatgttatttttccttttctgcatttcattgtcttgcaattatcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTGTCCCTGCACCACTTATGCTGCCAAAAGCACC

Basic information

species Zea mays
transcript GRMZM2G017089_T02
intron # 2
splice site 3'
intron type U2

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|76013838|gb|DT941008.1|DT941008
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211485186|gb|FL175528.1|FL175528
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGGAGA-GGCTCTAGGAAATGC-AT
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGG-AGAAGGCTCTAGGAA-TGCCAT
EST: gi|211485184|gb|FL175526.1|FL175526
EST:     AGGGCAAGGGTCCTGCGCCGCCATCTTTCA-CAGCTTTTGCATTGCCCAG                         AAACACA-GATACAAAAGATGCT
genomic: AGGGCAAGGGTCCTGCGCCGCCATCTT-CAACAGCTTTGGCATTGCC-AGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCT
EST: gi|76013076|gb|DT940246.1|DT940246
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|78123946|gb|DV542330.1|DV542330
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGTATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCTATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|78085590|gb|DV513983.1|DV513983
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211104567|gb|FL375458.1|FL375458
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211482306|gb|FL175513.1|FL175513
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAAACACA-GATACTAAAGATGCTCACGGAGAAGGCTCTAGGAAAATGC-A
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAA-CACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAA--TGCCA
EST: gi|78089068|gb|DV517459.1|DV517459
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211482314|gb|FL175521.1|FL175521
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAA-AGCTTTGGCATTGCCAG                         GAAACACA-GA-ACAAAAGATGCTCAC
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAA-CACAAGATACAAAAGATGCTCAC
EST: gi|148951460|gb|EC897185.2|EC897185
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211479425|gb|FL175508.1|FL175508
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|94478034|gb|EB706992.1|EB706992
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|148943611|gb|EC888674.2|EC888674
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|149079798|gb|EE168796.2|EE168796
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|148950913|gb|EC896543.2|EC896543
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|71436555|gb|DR817605.1|DR817605
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAAGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|211482312|gb|FL175519.1|FL175519
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|148962621|gb|EE013511.2|EE013511
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
EST: gi|76019935|gb|DT947105.1|DT947105
EST:     GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAG                         GAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG
genomic: GCAGGGCAAGGGTCCTGCGCCGCCATCTTCAACAGCTTTGGCATTGCCAGgttaactttg ... atcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacatgttatttttccttttctgcatttcattgtcttgcaattatcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTGTCCCTGCACCACTTATGCTGCCAAAAGCACC
                                           ttatctt  CT-rich tract
        ttatttttcctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataactaaagccgaaaaattcagacaaattagtttgctagctgtgtacatgttatttttccttttctgcatttcattgtcttgcaattatcttgtcagGAACACAAGATACAAAAGATGCTCACGGAGAAGGCTCTAGGAATGCCATTGTCCCTGCACCACTTATGCTGCCAAAAGCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC