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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtggaatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA

Basic information

species Zea mays
transcript GRMZM2G006790_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 2
ttgtggaatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgc-----agATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA
   |   ||||   | |   ||   |  |  | | | ||| |  |     ||  |     ||  |||||  | || | |||| ||       ||||||     |||||||||||| |||||||||||||||||| | ||| |||| |||||||| |||||| ||||||| |||||||||||||||||||||  ||| ||||||||
---tattatataaatggttatgtcgtctttcaaatatttactgat--ttgtgcaaacaaacagcttctcactcatatatcaaaaacaaccttttttgctcctcagATGAAGATTCCAATGGCGAAATAGATAAACAAGAATTGAAGCATTGTTTCCAAAAGTTGGAAATTTCATTCACAGAGGAGGAGATAAATGACCTCTTTGA
















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|78112681|gb|DV531075.1|DV531075
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211172415|gb|FL359082.1|FL359082
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366894|gb|FL196959.1|FL196959
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366893|gb|FL196958.1|FL196958
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAGCATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366887|gb|FL196952.1|FL196952
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366892|gb|FL196957.1|FL196957
EST:     AAAATAGACGAGAGTTTCAGAAAATGCAAGACBSATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAA
genomic: AAAATAGACGAGAGTTTCAGAAAATGCAAGACT-ATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAA
EST: gi|211203216|gb|FL341877.1|FL341877
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGA
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGA
EST: gi|211023721|gb|FL334134.1|FL334134
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAAATAGATAAAGAGGAACTGAAACATTG
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAA-TAGATAAAGAGGAACTGAAACATTG
EST: gi|40334046|gb|CK368116.1|CK368116
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|60394800|gb|DN227670.1|DN227670
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366890|gb|FL196955.1|FL196955
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366891|gb|FL196956.1|FL196956
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366886|gb|FL196951.1|FL196951
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|148978865|gb|EE026354.2|EE026354
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211162599|gb|FL365711.1|FL365711
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGAT-CAAATGGCGAAATAGAT
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGAT
EST: gi|211366884|gb|FL196949.1|FL196949
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|78086237|gb|DV514630.1|DV514630
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|74234337|gb|DT642251.1|DT642251
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|74234338|gb|DT642252.1|DT642252
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366883|gb|FL196948.1|FL196948
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCG
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCG

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), 49 (downstream exon)
Score: 80

TCGCATGGAACCTCACTGAAATCGTTCGATAGCATTATCATGAAGTTCCCCAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 107

TCGCATGGAACCTCACTGAAATCGTTCGATAGCATTATCATGAAGTTCCCCAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

TCGCATGGAACCTCACTGAAATCGTTCGATAGCATTATCATGAAGTTCCCCAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 899

TCGCATGGAACCTCACTGAAATCGTTCGATAGCATTATCATGAAGTTCCCCAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA
                                            tgctttt  CT-rich tract
           ttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtggaatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - -gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg