Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

Basic information

species Zea mays
transcript GRMZM2G087598_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 3
cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatct-cattgatttgtggagtggaaat---ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
  |  ||  || |   |    ||  |   |||  |||  ||  | ||  || ||| ||||| ||   | ||   |||  |    |||||||    |||||| |||||||||||||||||||| || ||||||||||||||||| ||  | || |||||||||||||||||||| |||||||| || || ||||| |||||||| 
-gtaagagataatctgcatatttgctaactgtgcttttgtttattac--ttgcatatcaaaattccgtgcaactattcatatc-tggaaatgtattctttgtagAACTTTGACGCCTGGCCACGACCCTGTCCAAAAGGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACG

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g45820.4 (Oryza sativa), 3'ss of exon 3
cttttgatttattggactgcctttttgtatgtcttttccttggtaacca-ttccatgtcaaatttatct-cattgatttgtggagtggaaat---ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
 |    |     |   |||| | ||||       |    ||| | |  | || ||| ||||| ||   | ||   |||  |    |||||||    |||||| |||||||||||||||||||| || ||||||||||||||||| ||  | || |||||||||||||||||||| |||||||| || || ||||| |||||||| 
gtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatc-tggaaatgtattctttgtagAACTTTGACGCCTGGCCACGACCCTGTCCAAAAGGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACG

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g45820.3 (Oryza sativa), 3'ss of exon 3
---------------------------------cttttgatttat---tggactgcctttttgtatgtcttttccttggtaacca-ttccatgtcaaatttatct-cattgatttgtggagtggaaat---ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA----------------------------------
                                  || ||  | |    |   |||| | ||||       |    ||| | |  | || ||| ||||| ||   | ||   |||  |    |||||||    |||||| |||||||||||||||||||| || ||||||||||||||||| ||  | || |||||||||||||||||||| |||||||| || || ||||| ||||||||                                   
gtcttgttgcttaccatgaagttgggcatgcaatttgtgggtaagagataatctgcatatttgctaactgtgcttttgtttattacttgcatatcaaaattccgtgcaactattcatatc-tggaaatgtattctttgtagaactttgacgcctggccacgaccctgtccaaaagGTTACTTTGATCCCGAGGGGTCAAGCTCGTGGTCTCACATGGTTCATTCCAATGGACGACCCAACGCTCATCTCCAGGCAACAACTGTTCGCCAGAATTG

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G26230.1 (Glycine max), 3'ss of exon 3
--------cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
         |     | |   |   |    |||   | | | ||||    |||| || | |     || ||  ||| |   || |||         |  |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  |||||||  | ||||||||||| |||||||||||||| || || |  ||||| ||||| 
aagcaaaagtaccactgttaagtggtaaaatttaaaaagccgtttc---agtaaacaattctcaaaaagttgttctaaaacatctgtttt-----tacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGTGGTCAAGCTCGGGGTCTTACATGGTTCATTCCTAATGATGATCCAACT

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G09160.1 (Glycine max), 3'ss of exon 3
--------cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
          |   |    |  ||       |||  | |   ||||    |||| || | |     || ||  ||| |   || |||  |      |  |  ||||||||||||||| ||||| |||||| |||| |||||||| ||  |||||||  | |||||||||||||| ||||||||||| || || |  ||||||||||| 
caagcaaaactaccaccgttaagaggtaacatttaaaagcagtttc---agtaaacaattctcaaaaagttgttctgaaacatctgttta-----tacttgcttgcagAACTTTGACTCCTGGTCATGATGCTGTGCAAAAGGTAACACTAGTTCCTCGCGGTCAAGCTCGTGGACTTACATGGTTCATTCCTAACGATGACCCAACT

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G05820.1 (Glycine max), 3'ss of exon 3
cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccat--gtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
  | | | | ||    | |         |||  | |   |  | | |  ||        ||| |  |     ||| | |      |  |  | |  ||||||||||||||| ||||| ||||||||||| ||||| || |||||||||||  | || ||||||||||||||||| ||||| || ||    ||||||||||| 
-atataagtaataatccagaaaaaaca-atggttctcattcagaagctgtttttgcaaacaattccaaaaagttgttcttaaatatctatctgtacttgcagAACTTTGACTCCTGGTCATGATCCTGTACAAAAAGTAACCTTAGTTCCTCGCGGGCAAGCTCGTGGTCTTACTTGGTTCATTCCTGCTGATGACCCAACT

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G17070.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------cttttgatttattggactgcctttttgta------tgtcttttccttggtaaccattccatgt---caaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
                                                                              |  ||| | |||   | |          |      ||  | |   |  | | |  ||   |||   ||| |  |     ||| | |         |  | |  ||||||||||||||| ||||| ||||||||||| ||||| || |||||||||||  | || |||||||| |||||||| ||||| || ||    ||||||||||| 
gtaagccaaaaatcagtaaatgtgtacgatatgatggcaatggaagcaaggtgttattgcctatataaattcatgttacacttg-tatataaaagtaatccagaaaaaaacaatggttctcattcagaagctgttttttgtaaacaattccaaaaagttgttcttaaatacctatctgtacttgcagAACTTTGACTCCTGGTCATGATCCTGTACAAAAAGTAACCTTAGTTCCTCGTGGGCAAGCTCGGGGTCTTACTTGGTTCATTCCTGCTGATGACCCAACT

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S9_115V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------cttttgattt--attgga-ctgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatct-cattgatttgtggagtgga--aatctctt----tgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
               | |   |||   | || | ||||  |    | |  | | | | ||  |   | |   ||| | ||   | |  ||  |  | | |  | ||  ||  |  |    ||||| || ||||| || || |||||| | || |||||||||||| |  |||| ||||||||||| |||||||| || |||||||||||    || ||||| || 
gtacccctcattcaccatccaattgcaactgcagctgctctggcattttccctcttcctg-cagtaaatgtctgtgagatgcttttatatctaagtctagtatcgatcaactttgtgtggtgcagGACCTTGACACCAGGGCATGATGCGGTGCAAAAGGTTACCCTTATTCCCAGGGGTCAAGCCCGTGGTCTCACCTGGTTTATCCCAGGCGACGACCCTACC

upper sequence: GRMZM2G087598_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S156_30V6.1 (Physcomitrella patens), 3'ss of exon 4
---cttttgattt----attggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttat--ctcattgatttgtggagt------ggaaatctctt--------tgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
   |||||  |||    ||   | |||  || |   ||   |||| |||            |   ||  |||     ||||||  | |   |         ||||   ||        ||||| || ||||| || ||||||||| | || |||||||||||| |  |||| |||||||||||||||||||| || ||||| || ||    || ||||| || 
gtactttttctttcaccatccaattgcaattgtacctgcagtttcattgtctctggaaaatttctaaggttacggtgcattgacctctaaggcttattaataaattaattgtgtgaggtgcagGACCTTGACACCAGGCCATGATGCAGTGCAAAAGGTTACCCTGATTCCTAGGGGTCAAGCTCGTGGTCTCACCTGGTTCATTCCAGGCGAGGACCCCACC

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|78090967|gb|DV519341.1|DV519341
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|24934237|gb|CA452455.1|CA452455
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|76011446|gb|DT938616.1|DT938616
EST:     AAGAGCAAAAATCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTG
EST: gi|74235282|gb|DT643196.1|DT643196
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|149086842|gb|EE176390.2|EE176390
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|24934160|gb|CA452378.1|CA452378
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATNTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|149089171|gb|EE178359.2|EE178359
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|76011445|gb|DT938615.1|DT938615
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|78076092|gb|DV504526.1|DV504526
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|88754818|gb|DY538959.1|DY538959
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|37377001|gb|CF625070.1|CF625070
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|50334510|gb|CO529636.1|CO529636
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|13178114|gb|BG349372.1|BG349372
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG
EST: gi|32850222|gb|CD989903.1|CD989903
EST:     AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTG
EST: gi|6021243|gb|AW066171.1|AW066171
EST:     AAGAGCAAAAGTCTTGNTGCTTACCATGAAGTTGGGCATGCAATTTGCGG                         AACTTTGACGCCTGGCCATGATCCTGGCCAAAAGGTTACCTTAGTTCCAAG
genomic: AAGAGCAAAAGTCTTGTTGCTTACCATGAAGTTGGGCATGCAATTTGCGGgtaagagatg ... ctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA
                                            tctctttgc  CT-rich tract
             aaatttatctcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgatttattggactgcctttttgtatgtcttttccttggtaaccattccatgtcaaatttatctcattgatttgtggagtggaaatctctttgcagAACTTTGACGCCTGGCCATGATCCTGTCCAAAAGGTTACCTTAGTTCCAAGGGGTCAAGCTCGTGGTCTTACATGGTTTATCCCGATGGATGACCCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA