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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtattctgtattccgcatcctcattgttttagtcagcaatcagcatcatggtcatcttatctgaaagcatgcccatttggctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGATTCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGAAGAAGAGATTAT

Basic information

species Zea mays
transcript GRMZM2G118014_T05
intron # 11
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|60349355|gb|DN216328.1|DN216328
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|60359397|gb|DN226370.1|DN226370
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|67019925|gb|CO448674.1|CO448674
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTANAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|149079347|gb|EE168323.2|EE168323
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|60347948|gb|DN214921.1|DN214921
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|60348227|gb|DN215200.1|DN215200
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|71445994|gb|DR827044.1|DR827044
EST:     GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|24767722|gb|CA402862.1|CA402862
EST:     CAGGAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCG                         ATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAACAAAAGGAGGACAGGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
EST: gi|211168469|gb|FK981061.1|FK981061
EST:     GGCACAACTGAGGATGATAGGCG                         AACTAAAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA
genomic: GGCAAAACTGAAGATGATAGGCGgtatggtatt ... gctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaatcagcatcatggtcatcttatctgaaagcatgcccatttggctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGATTCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGAAGAAGAGATTAT
                                              ctctttt  CT-rich tract
                   atcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtattctgtattccgcatcctcattgttttagtcagcaatcagcatcatggtcatcttatctgaaagcatgcccatttggctcttttagATCTAGAGAGCAGAGCAAGGATCGAAACGGCCCGCCGTCCAGGGATAGAGATTCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGAAGAAGAGATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA