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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT

Basic information

species Zea mays
transcript GRMZM2G472625_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 8
gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
||| ||||  |||||    |    ||||| | || ||   |  |||| |||||| || | |  |||| |    | |||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||  ||||||||||| ||||||||||| |||||||||    
gtattgcatgatgttgtgcaagctacatttttttttttgccacgggtatttcttgtgttaacttgatattatggcagGTTCTTGGTACTCCAACCCGTGAGGAAATACGATGCATGAACCCCAACTATACTGAGTTCAAATTTCCTCAGATTAAGGCTCATCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
---------gtactgca-aaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
          | ||  |  | |||  | | |          ||   ||| | | | |  || ||  | |       | | | |||||||||||||||||||||| || ||||| || || || ||||| || || ||||| ||||| || || |||||||| || |||||||| |||||||||    
gtgatgtcccttctatatgagtgtctccatg-gattgcagaatatatctgcagagataattatttagat------gtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
----------gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
          ||  |    |||||| |   | |     |  ||    || | | |  | |  |||   | ||||| | | | ||||| ||||||| ||||| ||||| || || || |||||||||||||| || ||||| || ||||| || || || || || |||||||| ||||| |||    
gtgattccttgtctttgttaatgttaccctggattggatgaatctagctgctgaga-gataattac--taatgtg-ttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 8
gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttc-----ttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
    ||     | ||  | | |||   | | ||  ||  |         |||     | ||  ||  |   | | | ||||||||||||||||||| || || ||||| || || |||||||| || || ||||| || || || || |||||||| || |||||||| |||||||||    
---gtgatgtctctttgatattagtgttgccatgattgcagaatatatcttcagagatcattatttaggtgtcttcttgtagGTTCTTGGTACTCCGACTCGAGAGGAAATCCGTTGCATGAACCCAAATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttctta-tggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                             || ||      |||          | | |  | |||  ||     ||     | | |     ||  |  |   | |||||||||||||||||||| ||||| || || ||||| ||||| || ||||| || || || ||||| || || || || ||||| || |||||||||    
gtgaagtctcctttattagactaatggatgtgctcttttttgtctttggtattagactagaatctagtaaatatgttaccataagtacacttgctaccttgttttagGTTCTTGGTACTCCAACTCGTGAAGAAATTCGATGTATGAACCCGAACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
-----gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
        ||  |||   |       |  | |||  ||||||   |       |      ||  ||  || ||| |    ||||||||||||| ||||| || || || || || || ||||||||  | || || || ||||||||||| ||||||||||| ||||| |||||||||    
gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac--acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
gtactgcaaaatgttccaaagtagacattctat-tcttctaccggggtgtttct-tatggttatgtgatgtgcct----gtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
|| | |||  || |      |     ||      || ||| |   ||   |  | ||    | |||||||    |     ||||||||||||||||||||  | || || || ||||| ||||| || || |||||||| ||||||||||||||||| || |||||||| |||||||||    
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 8
gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctg----tagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
|| |      || ||      | || ||  | |  ||||   |     ||| |||   |  ||   | || |||     ||||||||||||| ||||| || || || || || || |||||||| |  |||||||| || |||||||| |||||||| || || || |||||||||    
gtgcaatttgatttttagtgtttgaaatcatgtagttctggtgat-catttgttaaattcttgcattttgtctggtggcagGTTCTTGGTACACCAACGCGGGAAGAAATTCGCTGTATGAATCCGAGTTATACTGATTTTAGGTTTCCACAGATAAAAGCACACCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------------gta-ctgcaaaatgttccaaagtagacattctattcttctaccggggtgttt--------cttatggttatgtga-tgtgcctgt-agGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                                                                                                           ||| |||  |  || ||      |       |||   |   |  |  ||  |        ||||||| ||  ||  |||   ||| ||||  | || || || || || |||||||||   ||||||||||| ||||| || ||||||| ||||||||| || ||||||||||| |||||||||    
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtact-----gcaaaatgtt-ccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                                         |||||     ||    |||  |    |  |   |  |||  | ||   || |||| | |||| |        | |    | ||||  | || || || || |||||||||||    ||||||||||| ||||| || ||||||| |||||| || || |||||||| || ||||||||     
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgt-ggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtact-gcaaaatgttccaaa--gtagacattctattcttctaccggggtgtttct-tatggttatgtgatgtgcctgt-----agGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                                         ||||| ||    || |    |  || |      | || |  | | | || || |   |||| |  || |  || | |||     ||||  | || || || || ||||||||||||   ||||||||||| ||||| || ||||||| |||||| || || |||||||| |||||||||||     
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------gtactgcaaaatgttccaaagtagacattctattcttctaccggg-gtgtttcttatggttatgtgatgtgcctgt-----agGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                                                |    ||    || |    ||  |   |    |  |  |   ||  |||  | |   | | |   || ||  | ||     ||||| | || || || || |||||||||||    ||||||||||| ||||| || ||||||| |||||| || || ||||| || |||||||||||     
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA----

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------------------------gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttctta-tggttatgtgatg-tgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                                                                                                                  | || |     ||      ||       | |   |  ||| |  | | || | | | |     || || ||     ||||  | || || || || ||||||||||||   ||||||||||| ||||| || ||||||| ||||||||| || |||||||| ||||||||||||    
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG----

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|18660957|gb|BM501137.1|BM501137
EST:     CACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAG                         GTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTAT
genomic: CACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTAT
EST: gi|6587591|gb|AW244909.1|AW244909
EST:     CACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAG                         GTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTAT
genomic: CACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

CCACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 83

CCACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

CCACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 106

CCACTGTTTCCGGGAGAGAGTGCTGTTGATCAGTTGGTAGAGATTATCAAGgtactgcaaa ... gtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT
                          tttcttat  TA-rich tract