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

gtgtgatttggtactgtggtgtcactttattcaagtttgtttttaggtgatcatgctcttaaaacatgtctgataatgacatttctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG

Basic information

species Zea mays
transcript GRMZM2G324540_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 11
gtgtgatttggtactgtggtgtcactttattcaagtt-tgtttttaggtgatca--------tgctcttaaaacatgt--ctgataatgacatttctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG
      | || ||||  ||   ||  | ||||||||| | |||| ||||| |||        ||||||| ||| |  |  || | ||| |  ||| | ||| ||||||||||| |||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||
-----gtgtgatactccgg---caactcattcaagttcttttttcaggtgttcatgcatgtctgctcttgaaataccttgctaacaatcatcttttt-tctctagTCAAATGTTGCAAAGTTTGAGGGGCATGTTGGACCAGTGACTGCTATGTCCTTCTCTGAAAATGGTTACTTCCTTGCG

upper sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 13
----gtgtgatttggtactgtggtgt-cactttattcaagtttgtttttaggtgatcatgctcttaaaacatgtctgataatgacatttctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG
         ||  | | |     | |      |||| || ||  |  ||  || |   || |||| |   ||   |   | |    |   |     ||| ||||||| || |||||||| || ||    ||   ||| || ||||| |||||||||||||||||||||||||| |||
gtaaaaactatgggcttccaaactatatgacctattaaaattattaattgtgt-acagtgttcttcat-tatagttttcatttttttggttgataatagGCAAATGTGGCTAAGTTTGATGGACACACTGGGGAAGTTACAGCTATATCTTTCTCTGAAAATGGTTACTTCCTCGCG

upper sequence: GRMZM2G324540_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 13
gtgtgatttggtactgtggtgtcactttattcaagtttgtttttaggtgatcatgctcttaaaacatgtctgataatgacatttct--atctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG
              |      | |  |  | |||||||    |  | || |     |||| |  ||  | |     |  | ||| |  || || || ||||||| ||||  ||||| || || || ||  | || |||||||| |||||||| ||||||||||||||||| |||
-------------gtaataaattatgtcttgcaagtttaacctgggttgttagaattctttattcacttatttctctttcttttgttaatttgcagGCAAATGTGGCAAGATTTGACGGGCACGTTGGGGCTGTAACTGCTATATCTTTCTCAGAAAATGGTTACTTCCTTGCG

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|33096397|gb|CF056391.1|CF056391
EST:     GAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAG                         TCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCT
genomic: GAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCT
EST: gi|60337485|gb|DN204458.1|DN204458
EST:     GAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAG                         TCAAATGTCGCANAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCT
genomic: GAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 207

ACAAGAGGGATATACATCTGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

ACAAGAGGGATATACATCTGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

ACAAGAGGGATATACATCTGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

ACAAGAGGGATATACATCTGCGTCTTTCCATCCAGATGGTCTTATCCTTGGAACAGGAACTACTGATGCTGTTGTTAAAATTTGGGACGTGAAGGCTCAGgtgtgatttg ... ctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaggtgatcatgctcttaaaacatgtctgataatgacatttctatctgtagTCAAATGTCGCAAAGTTTGAGGGTCATGTCGGACCAGTCACTGCTATGTCTTTCTCTGAAAATGGTTACTTCCTAGCG
                            gtctgat  putative branch site (score: 108)
                                          tttctatct  putative PPT
                   ttaaaacat  TA-rich tract