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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgatatccttcaatatattcaagccaaatatcagtaaatttaccctttgtttatccccccttttctccatcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA

Basic information

species Zea mays
transcript GRMZM2G168510_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 13
gtaagtttgatatccttcaatatattcaagccaaatatcagtaaatttaccctttgtttatccccccttttctccatcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA
|||||||  |    | |  | || ||     | || |  | ||  ||||      | | |    |  | || | | |  | |||||||||| |||||||||||||||||| |||||||||| ||||| || ||| | || | ||||| |   |||| ||| ||  |    ||   | | | |||  
gtaagttacaccgacattcaaattttt---tcgaacacaaata--tttag-----gctaaaggtctttattgttctttctttgaagCGAGTCACCAAGGGAAAGAAGCCACTCAAGATCGATCTCACCCCCTTCAAAGAATAATCTGGTCCAGTTGGTAGGAAATAATGGGCACACTTGCTTGGTT
















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|31362214|gb|CD446571.1|CD446571
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|60359317|gb|DN226290.1|DN226290
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|16927330|gb|BM080399.1|BM080399
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|60340487|gb|DN207460.1|DN207460
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|71307283|gb|DR789816.1|DR789816
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|76910910|gb|DV164091.1|DV164091
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|5871261|gb|AW017732.1|AW017732
EST:     CCATTGCGCAATCTGGAAGAGCTGNTGGAGGAATTAATTGCAATGGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|16917526|gb|BM073324.1|BM073324
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|60400102|gb|DN232909.1|DN232909
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|74236360|gb|DT644274.1|DT644274
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|60398159|gb|DN230975.1|DN230975
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|5325089|gb|AI783280.1|AI783280
EST:     CCATTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|4681194|gb|AI629864.1|AI629864
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|50323771|gb|CO518897.1|CO518897
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGCCCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|18164292|gb|BM334131.1|BM334131
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|211183212|gb|FL204166.1|FL204166
EST:     CCATTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|83279046|gb|DV943054.1|DV943054
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|71763878|gb|DR961815.1|DR961815
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|211051797|gb|FL187615.1|FL187615
EST:     CCATTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|33101621|gb|CF061581.1|CF061581
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|6022160|gb|AW067088.1|AW067088
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|50323793|gb|CO518919.1|CO518919
EST:     GGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGCCCTCACTCCGTTCCAG
genomic: GGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|12972513|gb|BG268019.1|BG268019
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
EST: gi|4730747|gb|AI649913.1|AI649913
EST:     CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCT                         CGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG
genomic: CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 196

CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 147

CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 182

CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

CCGTTGCGCAATCTGGAAGAGCTGTTGGAGGAATTAATTGCAATTGCTgtaagtttga ... tcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatatcagtaaatttaccctttgtttatccccccttttctccatcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA
              tttaccctttgtttat  CT-rich tract
        agtaaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgatatccttcaatatattcaagccaaatatcagtaaatttaccctttgtttatccccccttttctccatcatgtgaagCGAGTTACCAAGGGAAAGAAGCCATTCAAGATCGACCTCACTCCGTTCCAGGAGTGATCTGCTTTGGTTGATAGAAAGCACAATGCCACCATCCATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA