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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtagtttcgagactgatacagattaatgctttgcatgtgctttactattaacaaaccaaagcatgtggggaactgtagttgcaattggtaattccagcatgcattccacaatgtcacaaaacagctaaacgtaaatgtctgtatataagtgagataccaacatttttgcctattaatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA

Basic information

species Zea mays
transcript GRMZM2G151916_T01
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|60348444|gb|DN215417.1|DN215417
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|31363416|gb|CD447773.1|CD447773
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|60398739|gb|DN231555.1|DN231555
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|91875587|gb|EB405544.1|EB405544
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|60349644|gb|DN216617.1|DN216617
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|60400988|gb|DN233795.1|DN233795
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|18172689|gb|BM348077.1|BM348077
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|78545004|gb|DV622502.1|DV622502
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|20802617|gb|BQ293667.1|BQ293667
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|14569185|gb|BI097508.1|BI097508
EST:     GGTTGCCAAATGGAGGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|211420812|gb|FL269789.1|FL269789
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|211159258|gb|FL355922.1|FL355922
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|29545134|gb|CB605312.1|CB605312
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCTTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
EST: gi|95107793|gb|EB740022.1|EB740022
EST:     GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAA                         CTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT
genomic: GGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCT

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: 49 (upstream exon), 45 (downstream exon)
Score: 301

TGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

TGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

TGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

TGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagta ... taatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtaaatgtctgtatataagtgagataccaacatttttgcctattaatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA
                                          tattaat  putative branch site (score: 240)
                                          tattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtagtttcgagactgatacagattaatgctttgcatgtgctttactattaacaaaccaaagcatgtggggaactgtagttgcaattggtaattccagcatgcattccacaatgtcacaaaacagctaaacgtaaatgtctgtatataagtgagataccaacatttttgcctattaatttgcagCTAGCAAATGCCTCCCCGGAGCTCATCAACAGGCTGATCCCAGACCATGCTAGGCGGCATCTTGGGCTCACTTTATTGCCCACCGCTGGACCATAGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA