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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatatttggtacaatttgattacacacatttgcag

Basic information

species Zea mays
transcript AC196278.2_FGT004
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 5'ss of exon 8
GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatat-ttggtacaatttgattacacacatttgcag
|||||||||||||||||||| |||||||| || ||||||||||| || |||||||||||| | ||||||||||||||||||||  |     |||| |   | ||   | |  |   || ||| ||||  |  |||| ||| |||| || |||| || ||||||||||
GATTTCATACGTGAAGTGGACCCTGATATTATTATTGGATACAATATCTGCAAATTTGACTTACCCTATCTTATTGAGgtacaggatt--ttgtaaa---tacaatatctgcaatacatttggcaatttgggatatcttgttacagttagatttcatacatttgcag

upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G38800.1 (Glycine max), 5'ss of exon 8
GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatatttggtacaatttgattacacacat-ttgcag-----------------------------------------------
||||| || ||||||||||| |||||||| || ||||||||||||||||||||||||||| |||| ||||||||||||||   ||   || |  | | |    ||     ||||      |  |  | |    |  ||  || ||   | ||     ||  |||  |                                               
GATTTTATTCGTGAAGTGGACCCTGATATTATTATTGGATACAACATTTGCAAATTTGACTTGCCATATCTTATTGAGgtgtgatttgactttgaaattaaaaagtacacttagagttgatagctgtaacgttttgttattaaaaaaaggttgtgtgcaagttgttgcggttcctgttctaatataatttaatttgttattgccttgttttcag

upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G16110.2 (Glycine max), 5'ss of exon 8
GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatatttggtacaatttgattacacacat-ttgcag-----------------------------------------------
||||| || ||||||||||| || ||||| || |||||||||||||| |||||||||||| |||| ||||||||||||||          || |    |    | |    ||||      |  |  | ||   |  ||  || |||  | ||     ||  |||  |                                               
GATTTAATTCGTGAAGTGGACCCGGATATTATTATTGGATACAACATCTGCAAATTTGACTTGCCATATCTTATTGAGgtgttgacttgactttgagat---taaaacacttagagttgatagctgtaaggttttgttattaaaataaggttgtgtgcaagttgttgtggttactgttctaatatagtttaatttcttgttgtcttgttttcag

upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: AT5G63960.1 (Arabidopsis thaliana), 5'ss of exon 8
GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatatttggtacaatttgattacacacatttgcag-----------------------------------------------------------------------------------------------------
||||| || ||||| || |||||||||||||| ||||| || ||||| |||||||| ||  | || ||||| ||||||||||   ||||    |||| | | |   |||| | | |  ||    | ||| |  |  || | | ||     ||   |    ||  ||                                                                                                     
GATTTGATTCGTGATGTTGATCCTGATATCATCATTGGTTATAACATCTGCAAATTCGATTTACCTTATCTGATTGAGgtacttgaacat---tagattttac---ttttattgacggatcagta-tcacctctggttagcagaagcgtgtttttctttcttatagcattctatatgtaatattatgctatgctccgctgggtcatatggcacatgtatatgtgatggatctttaacctagaaaatatgctgttttctgattctcag

upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 5'ss of exon 8
GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaata-acacctgtagagtgttca------gattttttaggccaattgacaatcagccatatttggtacaatttgattacacacatttgcag-----
|| ||  |    ||||| ||||| ||||| || ||||||||||||||||| ||||||||| | ||||||||||| ||||||   || |   |  |  | |  | |      | |||  |  ||   ||    || | |   |||   ||     ||  ||    || | |        
GAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAGgtagggtatattgccatgtacttattatcaaacggtttcattcgctgcttcttgattatcttgattgactaattactggctaagtgcagtcgaccttcat

upper sequence: AC196278.2_FGT004 (Zea mays), 5'ss of exon 4
lower sequence: PP1S14_182V6.1 (Physcomitrella patens), 5'ss of exon 8
----------------------GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataacacctgtagagtgttcagattttttaggccaattgacaatcagccatatttggtacaatttgattacacacatttgcag--------------
                      || ||| |    ||||||||||| ||||| || |||||||| || ||||| ||||||||| | ||||||||||||||||||      || |  | |  |  |  | |  ||  | |   || |    ||    | |   | | || ||    ||   ||||||                 
GATGGTAGTGGTGGCTTCGCAGGAGTTCGTCAAAGAAGTGGATCCAGATATTATTATTGGATATAATATTTGTAAATTTGACTTACCCTATCTTATTGAGgtaagcggccatcaattgcttactttggtgattctgacttgtttatgcacatttgtgtacagaataaatta--cactatcatttggttcattttcttggtgt

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: 44 (upstream exon), 42 (downstream exon)
Score: 154

GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataac ... acatttgcagAGGGCTGAGGTTCTCAAGATAGCGGAGTTTCCAATACTTGGCCGAATCAGAAATAGTCGTGTTCGTGTCCGTGATACGACCTTTTCCTCGAG


Block sizes: 44 (upstream exon), 30 (downstream exon)
Score: 16

GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataac ... acatttgcagAGGGCTGAGGTTCTCAAGATAGCGGAGTTTCCAATACTTGGCCGAATCAGAAATAGTCGTGTTCGTGTCCGTGATACGACCTTTTCCTCGAG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 18

GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataac ... acatttgcagAGGGCTGAGGTTCTCAAGATAGCGGAGTTTCCAATACTTGGCCGAATCAGAAATAGTCGTGTTCGTGTCCGTGATACGACCTTTTCCTCGAG


Block sizes: 42 (upstream exon), 17 (downstream exon)
Score: 12

GATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAGgtacaataac ... acatttgcagAGGGCTGAGGTTCTCAAGATAGCGGAGTTTCCAATACTTGGCCGAATCAGAAATAGTCGTGTTCGTGTCCGTGATACGACCTTTTCCTCGAG