Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

Basic information

species Zea mays
transcript GRMZM2G056393_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 11
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
   ||||   ||||  ||    | |     | |||||||   | |||  |||| || ||||   || | |  |   |      | |||||||||||||| ||||||||||| ||||| || |||||||||||||||||||| ||| ||||| | || |||||  ||
--gtatctacttttctattttcaag-----aatgctatattaactttaataccatacatgtgacaaataattaattaaaataacatttcagTTTTCAAAGGCTCTGAATCGTTTCCAGAAAGAGGATCCTACTTTCCGTGTAGGTCTGGATCCAGAAAGTGGAGAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 6
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgtta--ccctagatgtcctaagtgaaaatacacct--atccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
||   | || | ||| ||  ||   || | ||  ||   |    ||||  |  |  |  ||  ||||| || |  |     |  ||  ||| ||||||||||||||| |||||||||||||||| || |||||||| || ||||| || |||||  | |||||||| |||
gtgagtaatttattttatgtaacatgt-caacccctgccctagatttgaaaaacgttgtatcacctaattggatttctctgtgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACATTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 11
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctag-atgtcctaagtgaaaatacaccta-tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
||   | || | ||| ||  ||   ||    |  ||    | | ||    |   | | ||  ||||| || |  |   |  | |  ||| ||||||||||||||| |||||||||||||||| || ||||||||||| ||||| || |||||  | |||||||| |||
gtgagtaatttattttatgtaacacgtcaaccccctgcctagatttgaaaaaagttgtatcacctaattggatttctcctgaattgcttacagTTTTCAAAAGCTTTGAATCGCTTCCAAAAAGAAGATCCTACTTTTCGTGTTGGCTTGGACCCGGAGAGTGGGCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 11
-----gtatatcatatttttcatcaaaagggtacgactgctatacat-agtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
      ||| | |  |||       |||    |  |    | | | | | | || |       |  |   || ||||| |  |  |  |  | | |||| || ||||| |||||||| ||||| || |||||||||||||||||||||||||||||| | ||||||||||||
gtaacttatgtgaactttgaagctgaaacaacaacatatttttcctttaatctggttttacgaaatttgcaactgaaa-tctattttccggtgttagTTCTCGAAAGCACTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 11
-----gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
      | | | |  |||      ||||  | |  |    | | | |   || |     || |  |    |    ||||  |  | |   | | |||| || |||||  ||||||| ||||| || |||||||||||||||||||||||||||||| | ||||||||||||
gtaacttctgtgaactttgaagctaaaacagcaacatatttttccttcaattctggttttaaacatttgcaactgaaatctattttttggtgttagTTCTCGAAAGCATTGAATCGATTCCAGAAAGAGGATCCTACTTTCCGTGTGGGTTTGGATCCCGAGAGTGGCCAG

upper sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 11
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttacc--ctagatgtcctaagtgaaaata--cacctatcccttt-cagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
                 | |  | ||  | | ||  |||   | ||  ||     ||    || | || |||   ||      ||||| | | ||||||||||| ||| |||||||||| || |  |||||||||||||||||||| || ||||| ||||||||||| |||
----------------gtgagtacggc-caattgagatatcaatttactttgtaactgatggtaccaaatgatggtaattttttatccttgtacagTTTTCAAAGGCTTTGAATCGCTTTCAGAGAGAGGATCCTACTTTCCGTGTTGGGTTGGACGCTGAGAGTGGGCAG

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|32930091|gb|CF034903.1|CF034903
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAA                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|6194594|gb|AW146698.1|AW146698
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAG                         TTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG
genomic: CTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTCTGGAGGACAGgtatatcata ... tccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG
                                       cacctatccctttc  CT-rich tract
                               tgaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcatatttttcatcaaaagggtacgactgctatacatagtttgttaccctagatgtcctaagtgaaaatacacctatccctttcagTTTTCAAAAGCTCTGAATCGCTTCCAAAAGGAGGATCCTACTTTCCGTGTGGGTTTGGATGCTGAGAGTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG