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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttcgcttctaccgtgcgcaacaaacagtcctctgcccatcctacatttgcatcccactaaatgtctctgcttttggtttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA

Basic information

species Zea mays
transcript GRMZM2G011893_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|37425230|gb|CF650352.1|CF650352
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|18964079|gb|BM660797.1|BM660797
EST:     TGTACGCCGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|19057799|gb|BM736466.1|BM736466
EST:     TGTACGCCGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGGTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|211421218|gb|FL403241.1|FL403241
EST:     GTACGCGGGAAATGACACGCTTTTSSGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: GTACGCGGGAAATGACACGCTTTTC-GAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|8383251|gb|BE056194.1|BE056194
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|211087671|gb|FL396338.1|FL396338
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|71446780|gb|DR827830.1|DR827830
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|149102642|gb|EE287999.2|EE287999
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
EST: gi|78122304|gb|DV540688.1|DV540688
EST:     TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGG                         TCTTCAGTTCAAAAGGTTGATCTTCAGACCGGAAAA
genomic: TGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 36 (downstream exon)
Score: 33

GGTATCTTGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 25

GGTATCTTGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA


Block sizes: 31 (upstream exon), 36 (downstream exon)
Score: 29

GGTATCTTGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA


Block sizes: 31 (upstream exon), 36 (downstream exon)
Score: 10

GGTATCTTGTACGCGGGAAATGACACGCTTTTCGAGTCCACTGGCCTCTACGGCAGGgtaatgttcg ... ttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccatcctacatttgcatcccactaaatgtctctgcttttggtttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA
                      cactaaa  putative branch site (score: 10)
                                            tttctc  putative PPT
         tacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttcgcttctaccgtgcgcaacaaacagtcctctgcccatcctacatttgcatcccactaaatgtctctgcttttggtttctcaacagTCTTCAGTTCGAAAGGTTGAGCTTCAGACCGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT