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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

Basic information

species Zea mays
transcript GRMZM2G110185_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 2
---agttctctatcaaat-----gttcttccattca---tcagctgctttaaagg---ttaagaaggtcct-tttgaattagcatacctgagatgtgccctcatacttaac-gcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
    || |||  ||||||     | |  || ||| |     | |||   || |||   ||  |    |||   |||    | ||| |     || ||  ||  || | ||  ||||| || || |||||||| || ||  ||||||||||||||||||||||  | || || ||||||||||||||||| || || |||||  | || 
gtgtgtgctc-gtcaaattctttgcttctcaatttaaatataactgtgctacaggtgcttgcgctattccaacttgctgcaacatgctc---atctgaactgttaatgaattgcagGAATTAAAGAGTCTGACACTGGATTGGCTCCACCTAGCCAGTGGGACCTTGTATCCGATAAGCAGATGATGCAGGAGGAGCAACCCCTGCAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 2
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctg---agatgt--gccctcatacttaacg-cagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
 |||   | | | || || | |   |  ||  ||  ||  | ||  ||      |  ||   | | ||| ||||    | ||||  ||   |  |  | ||   ||| || |||||||||||||| ||  | ||  |||| |||||||||||| | ||||| |||||||| |||||||| ||||| || ||  | || 
-gttgcat-ttatattttatgctgattgtc--ctaattgcacgg--aatctatgctgttaacacttgcaaacctcctcaaatgttagcttcctgatgttacaatagGTATCAAGGAGTCTGATACTGGATTAGCAGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAAGAGCAGCCTCTTCAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 2
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaaga--aggtccttttga-attagcatacctg---agatgtgccctc---atacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
         |   || || |    |  |   | ||   |||  ||   ||   | | || || | | | | | ||||    | ||||   ||     |  |||    ||| ||||||||||||||||| ||  | ||| |||| |||||||||||| | ||||| |||||||| |||||||| || || || ||  | || 
--------gttgcat-ttatagtttatactggttgtcctaattgtatggactggatgctgttaacacttgtacacctccttaaatgtttgcttcctgttgttacaatagGTATAAAGGAGTCTGATACTGGTTTAGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAGCAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 2
---agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
   | ||     |     | | | |   | |||      |  | |   |    |    ||| || | |    ||  ||  |  |  | |  |  ||   | ||| || |||||||||||||| ||  ||||| |||| |||||||||||| | ||||| ||||| || |||||||| || || || ||  | || 
gataattggtattttggggatttgctgattatct-taattgcataaactgcatactgtcttgtgtacttttgtaaatgttagatttctt--ttgttgttgtagGTATCAAGGAGTCTGATACTGGTTTGGCTGCACCAAGCCAGTGGGATCTTGTTTCTGATAAACAAATGATGCAGGAGGAGCAGCCTCTTCAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 2
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtc-cttttgaattagcatacctgagat-gtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
   | | ||  || ||||      | |      ||  | | |  |     |  || ||||  | ||||  |    ||| | ||    |||        ||||| || || ||||| || || ||||||||    ||||| ||||||||| | || ||||||||||||||||||||||| |||||||| || || 
--gtatgtaggaactgtttgatggtcctaatattgtgtgacatttcgcttacctctctttccatttagtttctaagagttagttgtgtcacggcatgagcagGAATCAAAGAGTCCGACACCGGGCTGGCAGTGCCTAGTCAGTGGGATCTCGTATCAGATAAGCAGATGATGCAAGAGGAACAACCATTGCAG

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 2
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
                                                    || | ||   ||   | | |  |   | |     | | |||  | ||||||| |||||||| || || || || ||  | ||||||||||||||| |||| || |||||||| |||||||||||||| || ||  | |||
----------------------------------------------------gtgcgttgcgat---cttgctgggcttttttgagcgtgcttttc-cagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

upper sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 2
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
                                                   |  | ||  || || ||    ||    || ||     | |||  | ||||||| |||||||| || || || || ||  | ||||||||||||||| |||| || |||||||| |||||||||||||| || ||  | |||
---------------------------------------------------gtgcgttgcgattttgctgggcttttttgagc----gtgcttttc-cagGGATCAAGGAGTCCGACACTGGTCTAGCAGCTCCTAGCCAGTGGGATCTGGTGTCTGATAAGCAAATGATGCAAGAAGAGCAGCCACTGCAA

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|149015235|gb|EE045022.2|EE045022
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|149015481|gb|EE045355.2|EE045355
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|101395193|gb|EB819526.1|EB819526
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|149087114|gb|EE176653.2|EE176653
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|211399660|gb|FL004434.1|FL004434
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|110209654|gb|EC891551.1|EC891551
EST:     GGTCGAGAAGGAGATCAAGGATATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCCCCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|30087195|gb|CB885403.1|CB885403
EST:     GGTCGATTTTTAGATCNAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|19437016|gb|BM953426.1|BM953426
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|211035074|gb|FL073374.1|FL073374
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|78085799|gb|DV514192.1|DV514192
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|211010592|gb|FL355819.1|FL355819
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
EST: gi|28930845|gb|CB334206.1|CB334206
EST:     GGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCNCAG-GGGATTTG
genomic: GGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGC-CAGTGGGATTTG
EST: gi|211283518|gb|FL004413.1|FL004413
EST:     GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTG                         GGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG
genomic: GGTCGAGAAGGAGATCAAGGAAATGGCCAAGAAAATCAACGACCTCTGTGgtgaggattt ... cttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA
                                            acttaac  putative branch site (score: 3)
           ttttgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttctctatcaaatgttcttccattcatcagctgctttaaaggttaagaaggtccttttgaattagcatacctgagatgtgccctcatacttaacgcagGGATAAAGGAGTCTGATACAGGGCTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAGCAGATGATGCAAGAAGAACAACCGTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC