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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatataatcaatttaaaggcccatttgcgcagttagcatttatattctgtctagctgtcctgatttagtgatttatactcatgaatatgtcagcc...

Basic information

species Zea mays
transcript GRMZM2G166345_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 5'ss of exon 10
GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatataatcaatttaaaggcccatttgcgcagttagcatttatattctgtcta-gctgtcctgattta-gtgatttatactcatgaatatgtcagcc
||| | |||||||||| | |||||||| | | ||| ||||| |||||||||||||||||||| |||  |||||| || ||||||||||| |||| || ||    |    |  | |    || |||      |   |  | |   ||| |  || || |||       || | | | |   |  |  | |  |  
GTCTTGTGTGCTTCAAATCAAGATCATACAGTTGTAGAGCCATTGATTCCTCCAGAAGGAGCTAAGCCTGGAGAGCGTATTTCATTTGCAGGgtaagaattatgttgtatagatgtgatatctgcattaaaattttaaaaaacgtgtttgtgcagttctggggagcatgttctgttcaatttgacctatttg--

upper sequence: GRMZM2G166345_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv13s0067g03060.t01 (Vitis vinifera), 5'ss of exon 10
GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatataatcaat-ttaaaggcccatttgcgcagttagcatttatattctgtct--agctgtcctgatttagtgatttatactcatgaatatgtcagcc
|| || |||||||| | |||||||||  ||| ||| ||||||||| | ||||||||||| ||||| ||||| |||||  |||||||| |||||| || ||   |  | |  ||||  |  | || |     | || |  ||  | ||  |  || |||  | |  |  ||    |     |  ||||||  |   
GTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGGgtaagcatgctaaaattactaaaaactaacttacatccattgcctgaatgctttgcatgcagttgttgtaaaattttgga--aggagtaccaatatgataag-
















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|4874363|gb|AI673883.1|AI673883
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|4573130|gb|AI586779.1|AI586779
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|12972445|gb|BG267985.1|BG267985
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|33098108|gb|CF058068.1|CF058068
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211244774|gb|FL481676.1|FL481676
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|33095166|gb|CF055160.1|CF055160
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|213173994|gb|FM188956.1|FM188956
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|4628469|gb|AI619343.1|AI619343
EST:     AAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: AAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|89247315|gb|DY619101.1|DY619101
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|18173735|gb|BM349123.1|BM349123
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|37381901|gb|CF627857.1|CF627857
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|33095762|gb|CF055756.1|CF055756
EST:     TTGATTCCTCCAGAAGGAGCCAAAATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|5005650|gb|AI711712.1|AI711712
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|91873662|gb|EB403619.1|EB403619
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
EST: gi|211165085|gb|FL207333.1|FL207333
EST:     TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG                         GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA
genomic: TTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGA

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), 47 (downstream exon)
Score: 183

GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 177

GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 184

GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 140

GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatat ... tgatgtgtagGTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGGgtcagtatataatcaatttaaaggcccatttgcgcagttagcatttatattctgtctagctgtcctgatttagtgatttatactcatgaatatgtcagcc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA