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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggagagctgcgtatcattatattagaaggagaaatcttgttagacacgctcttactttttcactgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG

Basic information

species Zea mays
transcript GRMZM2G104958_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104958_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g01650.2 (Oryza sativa), 3'ss of exon 5
caggagagctgcgtatcattatattagaaggagaaatcttgttagacacgctct--tactttttcactgtaatatttgaaactcgttt----ctgggtttgtgcagGCTGC---TCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG
           | |  ||||  || |     | | || ||  |   ||   | |      | |  |   | |   ||||| ||   ||     |    |||   ||||||    | ||||  | ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| | |||||   
------cttgacttcccattccatgattttcatacattttagttctcatcttttatcgtgtgtggatcattagggttgaacctaacttagcatttttgttggatagGCTGTGAATTCTAAGAGCATGCTGGATGATTGGCAAGAGAATTTGGCTATTATAACTGCAAACAGGACGAAAGGTGATGATCTTGTAATTACGCACCTTG---

upper sequence: GRMZM2G104958_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
-------------------------------------------caggagagctgc---gtatcattatattagaaggag-aaatcttgttagacacgctcttactttttcactgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG
                                           ||    || ||    ||  ||||   | |  ||    |||  || || |   |  | | | ||     ||  ||  ||||    | | || |   |||   |||| ||   | || |||||||| ||||| ||| | |||||| ||||| | ||||| |||||||| || ||||||||||| ||||||||||  | |||||| |
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgtt-gcttttccattt---cagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG

upper sequence: GRMZM2G104958_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
--caggagagctgcgtatcattatattagaagga-gaaatcttgttagacacgctcttactttttca---ctgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG
     |  | | |    |  | | || |        |||| || || | ||  |  || |||   ||   || |    |||     |   |     |    |   |||||   | ||  ||||||| ||||| ||| ||||||||||||| || ||||| || ||||| ||||||| |||||| ||||| ||||  |  |      
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttgcttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC------

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|211290289|gb|FL278532.1|FL278532
EST:     TTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAG                         GCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAAT
genomic: TTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAAT
EST: gi|211290286|gb|FL278529.1|FL278529
EST:     -GAGAATCCCTGTTA-CAGTGGTTTGTCTTCTCCCCA-CAGCCTGTAGAG                         GCTGCTCCTAAAG-TATGCTGNATGACTGGCAAGAGAATT
genomic: TGAGAATCC-TGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATT
EST: gi|211290284|gb|FL278527.1|FL278527
EST:     TGAGA-TCCTGTTAACCAGGGGTTTGTCTTCTCCCCA-CAGCCTGTAGAG                         -CTGCTCCTAAAGGTATG
genomic: TGAGAATCCTGTTAAC-AGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATG

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: 47 (upstream exon), 49 (downstream exon)
Score: 78

GAGGACACTGTGCCTTCTTATTGCTGGACAACCTGCAGATGTTTTCAGTTTTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

GAGGACACTGTGCCTTCTTATTGCTGGACAACCTGCAGATGTTTTCAGTTTTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GAGGACACTGTGCCTTCTTATTGCTGGACAACCTGCAGATGTTTTCAGTTTTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 85

GAGGACACTGTGCCTTCTTATTGCTGGACAACCTGCAGATGTTTTCAGTTTTGAGAATCCTGTTAACAGTGGTTTGTCTTCTCCCCAACAGCCTGTAGAGgtaatattat ... gtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacgctcttactttttcactgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG
     ctcttac  putative branch site (score: 85)
                    tgtaatatttgaaa  TA-rich tract