Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGAAGCTTG

Basic information

species Zea mays
transcript GRMZM2G006790_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006790_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 2
---aatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgc-----agatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGAAGCTTG
    ||||   | |   ||   |  |  | | | ||| |  |     ||  |     ||  |||||  | || | |||| ||       ||||||     |||||||||||| |||||||||||||||||| | ||| |||| |||||||| |||||| ||||||| |||||||||||||||||||||  ||| ||||||||      
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|71428676|gb|DR809726.1|DR809726
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGC
EST: gi|211172415|gb|FL359082.1|FL359082
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366887|gb|FL196952.1|FL196952
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211162599|gb|FL365711.1|FL365711
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATCAAATGGCGAAATAGAT
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----TCAAATGGCGAAATAGAT
EST: gi|211366891|gb|FL196956.1|FL196956
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|148978865|gb|EE026354.2|EE026354
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366886|gb|FL196951.1|FL196951
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366894|gb|FL196959.1|FL196959
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|71428675|gb|DR809725.1|DR809725
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGC
EST: gi|211023721|gb|FL334134.1|FL334134
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAAATAGATAAAGAGGAACTGAAACATTG
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAA-TAGATAAAGAGGAACTGAAACATTG
EST: gi|211366890|gb|FL196955.1|FL196955
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
EST: gi|211366884|gb|FL196949.1|FL196949
EST:     CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTG                         ATGAAGATTCTAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC
genomic: CAAAATAGACGAGAGTTTCAGAAAATGCAAGACTATCTTCGAACAGTTTGgtgagttctg ... gcagatgaagAT-----T-CAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGAAGCTTG
                 cgttgat  putative branch site (score: 5)
                                        cttttgc  putative PPT
     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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattcgttgacttgcgctaatggagacaattatttttgacactgtcagttttcatgttctcgttgatgtgtcaagaagtggtgcttttgcagatgaagATTCAAATGGCGAAATAGATAAAGAGGAACTGAAACATTGTTTTCAAAAGCTGGAAATCTCATTCACAGAGGAGGAGATATGTGATCTCTTTGAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - -gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggtgc