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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag

Basic information

species Zea mays
transcript GRMZM2G382240_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 5'ss of exon 8
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgc---aacccacttgtagttgcttagtttaaaacatcctaaat-agttactaattggttctgcatcttggacttgcag
||||||||| || ||||||||||||||||||||||| ||||| ||||||||| ||||||||||||||  |    |    ||| | ||| ||   |    |||||||| | | ||||||| | || ||| |       |  ||||||
ATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGGgtatgtcttgtaggtgcttct-gtttctatttccggaacatccttactgagttactgactgattcgg-------gggttgcag

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA03G16660.2 (Glycine max), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaac-atcctaaatagtt--actaattggttctgcatcttggacttgcag-----------------
        | |||||||||||||||||| |  ||||||| ||||| |||||| |||| ||||||||   |||  | | ||  ||||  |    | |||   ||  || ||  ||    || ||   |||  |  || ||| |   |                 
--------ATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggagcatgctatttcaagtttatgcactgaaatttattttatattatttggttattttcatcttgacatttgacctatggcacatccctccaaacca

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G17810.2 (Glycine max), 5'ss of exon 9
-------------------------------------ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag-------------------------
                                      |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| ||||||||   | |    | ||   || |  |||||   |    ||||||| |||  ||    |  || |  |   |  |  |                          
TATCATTTCTATGGTTGACTTGATTGTCCACTTACAGGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttca-agttt---atgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G41330.1 (Glycine max), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgta------ttgcaacccacttgtagttgcttagt--ttaaaacatcctaa--atagttactaattggttctgcatcttggacttgcag-----------
 |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| ||||||||      |  ||  |||  | ||    || | |  ||| || | | |||  | | | ||   ||        |   |  | | | ||           
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATGTTGACTCTGAAGGAAGGgtaggagcatgacattccaagtttatgcactaaataattataaaaccttaatgaaaatgacatgtttaactattactgtccattaggaggcccaaacatt

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA03G16660.1 (Glycine max), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaac-atcctaaatagtt--actaattggttctgcatcttggacttgcag-----------------
 |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| ||||||||   |||  | | ||  ||||  |    | |||   ||  || ||  ||    || ||   |||  |  || ||| |   |                 
GTACACAGATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggagcatgctatttcaagtttatgcactgaaatttattttatattatttggttattttcatcttgacatttgacctatggcacatccctccaaacca

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G17810.3 (Glycine max), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag-------------------------
 |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| ||||||||   | |    | ||   || |  |||||   |    ||||||| |||  ||    |  || |  |   |  |  |                          
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGGgtaggactaggagcatgccatttca-agttt---atgcactaaataattataaaactataatgaaaatgacatgtttaactattacggtccattaggaggccca

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA01G25940.2 (Glycine max), 5'ss of exon 9
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtatt-gcaacccacttgtagttgcttagtttaaaac-atcctaaat-agttactaattggttctgcatcttggacttgcag------------------
 |||||||| ||||||||||||||||||||  |||||||  |||| ||||||||||| ||||||||   |||  ||| ||  ||||  |    | |||   ||  || || | ||  | |||       | | |||| |                        
GTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGGgtaggagcatgccattttaagtttatgcactaaaagttattttatattatttggttattttcatctctttttggtcaaattttattctcctaccataagt

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G79210.1 (Arabidopsis thaliana), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgt----attgcaacccacttgtagtt-gcttagtttaaaacatcctaaatagtt-----actaattggttctgcatcttggacttgcag
 |||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||||    |||   ||| |    || ||  |||  |||  |   | |  |||   |      |  ||    || |  ||||    |  |||
GTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGGgtgagcatttttaccaaaacttaatttactttatttccagagttcagaatttctcaaaagcctataacctccgtgtctt---ttcacag

upper sequence: GRMZM2G382240_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 5'ss of exon 10
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgta--ttgcaacccac-ttgtagttgcttagtttaaaacatcctaaatagttactaattggt-tctgcatcttggacttgcag-----------------
 |||||||| || ||||| ||||| |||||||| ||||| || ||  |||| ||||||||||||||  |   || | || || |  ||    |||      | |  |||  ||     | ||  | |    |  |   |||  |||                 
GTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGGgtaagtacaaatctacattattattagaaagtagttcgcctgataatcagagttcacttcatattcatagatcacactctcagtgtgactgatagattac

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|29945873|gb|CB815863.1|CB815863
EST:     TGCAATTTTGACTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: TGCAATTTTGACTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
EST: gi|9953260|gb|BE639843.1|BE639843
EST:     AATTTTGACTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: AATTTTGACTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
EST: gi|32944790|gb|CF049609.1|CF049609
EST:     GCAATTTTGACTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: GCAATTTTGACTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
EST: gi|108954176|gb|EC365039.1|EC365039
EST:     ATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: ATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
EST: gi|5555273|gb|AI881224.1|AI881224
EST:     CTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: CTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
EST: gi|15352985|gb|BI502596.1|BI502596
EST:     ACACTGCAATTTTGACTTTGAAAGAAGG                         ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC
genomic: ACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaac ... ggacttgcagATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGGgtattgcaacccacttgtagttgcttagtttaaaacatcctaaatagttactaattggttctgcatcttggacttgcag

- - - - - - -  GGAGCT
- - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG