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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccagtatatcgccaaagatgctgtctgtattcgtggttaaatgcatgcatccagtgttaacactgtcattatatcaccaaagatgcgcatattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT

Basic information

species Zea mays
transcript GRMZM2G023392_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023392_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g44560.1 (Oryza sativa), 3'ss of exon 1
-gccagtatatcgccaaagatgctgtctgtattcgtggttaaatgca-tgcatccagtgttaacactgtcattatatcaccaaagat-----gcgcatattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT
      |  |||   ||   |  | | |  | || |  ||| ||  | |||||| | || |       ||| ||||| ||||||  |     | | ||||||  |||||  |||||||||| | |||||||||||||||||| ||||||||||||||  | ||| |||| |  ||||| |||||  |||||   ||||| |||||||
cattgatggatc--taatacttttttgttcagtcctt-ttatatataatgcatcaaatgatgg----atcagtatataaccaaaattcttctgtgtatatttcctagGCCACAGCTGGTGGGTACATGGTAGCATTTGCCGGTAGGAAGTATGCAGCCCGGTCTGTTCCAACCTTTGTGTCCAATTCCTCATATACAGTCTCCAGCT
















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|76285613|gb|DV025181.1|DV025181
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198227|gb|FL002575.1|FL002575
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|14569390|gb|BI097713.1|BI097713
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGC
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGC
EST: gi|76016614|gb|DT943784.1|DT943784
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198221|gb|FL002569.1|FL002569
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGTAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|149087946|gb|EE287203.2|EE287203
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|8665537|gb|BE186353.1|BE186353
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|149087948|gb|EE177188.2|EE177188
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|18178640|gb|BM379850.1|BM379850
EST:     GGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: GGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198219|gb|FL002567.1|FL002567
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|78111842|gb|DV530239.1|DV530239
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|78105739|gb|DV524157.1|DV524157
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|149076826|gb|EE165479.2|EE165479
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211200767|gb|FL002581.1|FL002581
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|74240127|gb|DT648041.1|DT648041
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198228|gb|FL002576.1|FL002576
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|148959394|gb|EE010767.2|EE010767
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|31353180|gb|CD437537.1|CD437537
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|32870803|gb|CF010485.1|CF010485
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|101399855|gb|EB821775.1|EB821775
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198225|gb|FL002573.1|FL002573
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|116821439|gb|EC864739.1|EC864739
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|76285614|gb|DV025182.1|DV025182
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|211198226|gb|FL002574.1|FL002574
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|148973610|gb|EE024718.2|EE024718
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
EST: gi|101399860|gb|EB821776.1|EB821776
EST:     TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCA                         GCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT
genomic: TCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 56

CCGCCTCAACCTCGCTGCCTCCGGGCAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT


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

CCGCCTCAACCTCGCTGCCTCCGGGCAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

CCGCCTCAACCTCGCTGCCTCCGGGCAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CCGCCTCAACCTCGCTGCCTCCGGGCAGCTCGCCGTCTTCCGCCCCAAGGTCGACGAGATCTCCCTCCTCACCATCAACACCACTACCGGATTCAACCCAgtaagcgatc ... tattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatccagtgttaacactgtcattatatcaccaaagatgcgcatattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT
          tgttaac  putative branch site (score: 68)
                                            atattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccagtatatcgccaaagatgctgtctgtattcgtggttaaatgcatgcatccagtgttaacactgtcattatatcaccaaagatgcgcatattttgtagGCTTCAGCTGGTGGATTCATGGTAGCATTTGCCGGCAGGAAGTATGCAGCTAGATCTATTCCGATATTTGTATCCAACACCTCAGTCACAGTGTCCAGCT

- - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgcgc