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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

Basic information

species Zea mays
transcript GRMZM2G136296_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 2
----tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
    | |     || |     ||| |||| ||  |||||           ||   |||  || | |  |||   | ||     |     ||  || ||||  ||||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| ||||| ||||||||||| |||
tttctcgtgtagttcaaaacttatgaatt-ta--ttcttattctccagtctttccctccctttt-tgctttatgtattgaaactaaaactttgtgctgctcaagGCTCGCCGTGGTGGAGTGGATGAACCATTTGCTTGGGAAAGCAGGGAGTTTCTAAGGAAACTCTGCATAGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G38010.1 (Glycine max), 3'ss of exon 2
--------------tggaactatttactgagtatcaattgtagcttcttgacaatt---gacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
              | ||  | ||| |   | || ||||  | |   |  | ||||   | |  | |  | ||| || |||| ||  |||||   || ||| | |    |  | ||||| ||| | ||||| || || ||||| ||||||||||||||||||||||||||||||||||||||||||||||||
gtacttttagttatttgactttttttcattggattaatta-atcaattaaataatttaaggctctgtgttaattgctttagtgttgtttttt---ttttttttgcgaattattgtagGCGCGTAGAGGTGGTGTGGACGAGCCTTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgct-----tgtttattcatggtgcta--tagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                                 |   | | ||| | | ||   ||||      |  ||| |||||   ||  |   | ||||   || || |  || || |     | ||| || |      |   ||||| ||| | ||||| || ||||||||||||||||||||||| |||||||||||  ||||||||||||| ||||||
gtaattttacttgattcatggatattttgttgtaactatgaactgaaattgttttgaaatgcttctgtatcgattttgtgttaataatgttttccgtgttctaatttcgaaat--tgaaaattgctttttgtgctacttctggggtgtttacattacgttaaagctctttgtttaaaaaatttgctagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCATGGGAAAGTAGAGAGTTTCTACGGAAGCTCTGCATTGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G17050.4 (Glycine max), 3'ss of exon 2
--------------tggaactatttactgagtatcaattgtagcttcttgacaattgacattctt---ctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
              | ||  | ||| |   | || ||||  | |   |  | |||| | |   ||    | ||| || |||| ||  |||||   || |||    || |||   ||||| ||| | ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtagttttagttatttgactttttttcattggattaatta-atcaattaaataatttaaagctttgtgttaattgctttagtgttttttttttttttttttgcgaattgtg--gtagGCGCGTAGAGGTGGTGTGGACGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------tggaactatttactgagtatca-attgtagcttcttgac---aattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgct--atagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                              | |   | | |  ||  |  |  ||| ||  |||   |    || ||   |   |   | | ||   || || |  ||    || ||| || |      |  |||||| ||| | ||||| || |||||||||||||| |||||||| |||||||||||  ||||||| ||||| ||||||
gtaattttacttggttcatggaattgaaattgctgtgactgtgaattgaaattcttttgaaattctgttgtaccgattttgtggtttatgatgttttccgtattctaatttcaaaattgaaaatgctttctgtgctactgctgaggtgtttacattaaagttctttgtttaaaaattttgatagGCGCGTAGAGGTGGTGTAGATGAGCCGTTTGCGTGGGAAAGTAGAGAGTTTCTACGGAAGCTTTGCATTGGGAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G07350.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------------------------tggaactatttactgagtatcaattgtagcttcttga-caattgacattcttctcatttctctagttttcatttt---tcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                                                                                             ||    | ||   |   ||    || |    |||| | |    ||   | || |  ||| |     ||  || |    | | |||||| ||| |     | ||||||||  | || ||  | |||||||| |||||||||||||||| ||| ||| ||||||| || |||||||| |||
gtgagttttaatctcaagttttttttaccagatattagtgtttgaaacaaaagcttgtgatcatcacaaccaatcaaaaaatctttttgatattgatttttttcttttcatactgcttatgaagtcttaaaccgcagattatattattttttgttggaattaaatgtcatgttgtttgttttttcct--ctttttagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAAAGAATTTTTGAGGAAACTTTGCATAGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 2
--tggaactatttactgagtatcaattgtagc----ttcttgacaattgacattcttctcatttct--ctagttttcatttttcgc-ttgttta--ttcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
    |   | || |   || ||   || |  |     | || || |   | | | |||   ||  |  ||| || | || |||| | ||||||   ||     || |  |||||||  | || ||  | |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || |||
gtcagctttgttaaaaaagcattccttttcacaactctttttactaacaaaagttttcaatttcatagctacttattatgtttctcattgtttggtttgcctttgtttcagGCTCGCAGAGGAGGTATAGATGAGCCTTTTGCATGGGAAAGCAGGGAGTTTCTAAGGAAGCTTTGCATTGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 3'ss of exon 2
----------tggaactatttactgagtatcaattgtagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
            ||||  |||  |  || |||  |||   |  |  |   |    |||   || ||  ||     | || ||||   ||   | |||| |        |||| ||| | ||||||||||||||||||||||||||||| |||||||||| | | |||||||||||||| || |||
ggattttgttaagaacattttgttttgt-tcagctgtga-taataaatggtattgattagacttatgactgggagtctctttttctcctctctcattcct--------agGCCCGTAGGGGTGGAGTTGATGAGCCGTTTGCATGGGACAGCAGAGAGTATTTAAGGAAGCTCTGCATTGGAAAG

upper sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 1
--tggaactatttactgagtatcaattg--tagcttcttgacaattgacattcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
  ||| | || | |      |    ||   |   ||||  | | |  | | |||| |  | |  |  |   | ||||||   |||  |||  || |  |||||||| ||| | |||||  ||||||| || ||||||||||| || ||||||| | ||||||| ||||||||||| |||
tttggcattactaataccacactttttaaatgaattctctatattccatactcttattctgtaccctgacctgattttt---ttgaatatctattg-actatagGCCCGTAGAGGTGGTATTGATGAACCATTTGCATGGGATAGTAGAGAGTATTTGAGGAAACTCTGCATAGGAAAG

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|71441098|gb|DR822148.1|DR822148
EST:     TCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTG                         GCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTT
genomic: TCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTGgtaagatcaa ... ggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTT




















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), 48 (downstream exon)
Score: 250

TGTGACATCTGGGGATTGTCTTGTAATTATGGGGTGCACAAAGGCTGAGATCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTGgtaagatcaa ... ggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TGTGACATCTGGGGATTGTCTTGTAATTATGGGGTGCACAAAGGCTGAGATCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTGgtaagatcaa ... ggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

TGTGACATCTGGGGATTGTCTTGTAATTATGGGGTGCACAAAGGCTGAGATCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTGgtaagatcaa ... ggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

TGTGACATCTGGGGATTGTCTTGTAATTATGGGGTGCACAAAGGCTGAGATCGAACCTGAGAAGTCCATCACCTTATCCTACCTTATGGCCCCAAGGCTGgtaagatcaa ... ggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttctcatttctctagttttcatttttcgcttgtttattcatggtgctatagGCTCGTCGTGGTGGAGTTGATGAGCCGTTTGCATGGGAAAGCAGAGAGTTTCTGAGGAAGCTCTGCATAGGGAAG
                tagttttcattttt  TA-rich tract