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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatactaaacatctcatag

Basic information

species Zea mays
transcript GRMZM2G142249_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g30740.1 (Oryza sativa), 5'ss of exon 9
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatactaaacatctcatag
|||||||||||| ||||||| |||||||| |||||||||||||| |||||||| |||||||||||  ||||||||||||||||||||||||| || ||||||  ||||| ||| |  |||||  |  ||||| |  |||| |         ||  ||     ||||||  |||  | ||||| |   ||
GAGAAGGACCAGTTATTTTGCCTTCTTGGGCCCAATGGAGCTGGTAAAACAACAACAATCAGTTGCTTGACTGGAATCACACCAATTACAGGCGGCGATGgttggtatctttcttaaaagcaaaag-cttgtatagttgtattgttttg-taatatc-----taataagccattttgaacat-tggcag

upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G20360.2 (Glycine max), 5'ss of exon 9
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattc--ttgtttctttg----tctcaaaacaacaacttccatact-aataata-catactaaacatctcatag----------
|  ||||| ||| ||||||||||||| || |||||||||||||||||||| ||  | || | |||  |||| ||  | || ||| | || |  || |||||| |   ||  |   ||   | |   |    |  | | |||    |     ||  | || | | ||| | || || |  ||  |||   | |||             
GCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGCTTGACAGGGGTAACTCCAGTAACTGATGGAGATGgtgatactctctttctgtgtctgttgttaactactacattgaacattcattaatcaaaattacaatagtcaacaagagtatgttaacattttcaatttctttaacag

upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G34140.2 (Glycine max), 5'ss of exon 9
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatactaaacatctcatag---------------------
|  ||||| ||| ||||||||||||| || |||||||||||||||||||| ||  | || | |||| || | || || || ||| | || |  || |||||| | ||   |  ||        |  ||||           |  ||    ||     || | | | ||||      ||   | |  ||                      
GCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTCCAGTAACTGATGGAGATGgtga-tactctctatccgtctctctgtctttaacaaccacattgaacattcattaatcaaaattacaataatcgagaagagtatgttaacatttccaatttctttaacag

upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT3G47730.1 (Arabidopsis thaliana), 5'ss of exon 9
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatactaaacatctcatag--------------
|  || || ||  |||| ||||||||||| |||||||| || || ||||||||||| |||| |||| |||| ||  |    ||| |||| || |||||||||||| ||    | ||| | |    ||||||||||| | ||  | ||       | | |  |   |    ||||||||  |||||   |              
GCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTCCAGTTACTGGTGGTGATGgtaag-ataaagc-ttgca-cttttttcttgtttctgtttcatagaagctagtgtcctaagccttttcaccatactaa-tatctctctggttggctttaacag

upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT5G61690.1 (Arabidopsis thaliana), 5'ss of exon 7
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatc-gttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatac-taaacatctcatag--
|  || || ||| | |||||||||||||| || ||||| || || ||||||||||| || |||||| ||||||| || |  ||| |||| || |||||||||||||||| ||| |  || | ||||     |||       |||||| ||       |||| |||||||||   |  | |    || | |   
GCCAAAGATCAGTTGTTTTGTCTTCTTGGACCTAATGGCGCGGGGAAAACAACTACTATTAGTTGTTTGACTGGCATAAATCCAGTTACTGGTGGTGATGgtaagtatctgtttagagaggaagcaaaaa-gtt-------ctcaaagcatttttaaccattctaataatatccatgtgattgacttaaacag

upper sequence: GRMZM2G142249_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv17s0000g05850.t01 (Vitis vinifera), 5'ss of exon 9
GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcgttcattgaagcagcattcttgtttctttgtctcaaaacaacaacttccatactaataatacatactaaacatctcatag----
   ||| | || ||||||||||| ||||| |||||||||||||||||||| |||||||| | |||  |||||||||| || ||| | || |  |||||||||||   ||  |  | |        || ||  ||  || | |  |   ||     |  |    |   | |  ||  || | |||  | |    
CCAAAGAATCAACTATTTTGTCTCCTTGGACCCAATGGAGCTGGAAAAACTACTACAATTAATTGCTTGACTGGAATTACCCCAGTCACTGAGGGTGATGgtaatgttcaattttcgtgt-----ttattaatttcttctatgtagttaatggaatgtacttgagctacat-tatgaaccgtcttgttgacag

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), 48 (downstream exon)
Score: 14

GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcg ... catctcatagCATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 195

GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcg ... catctcatagCATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 406

GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcg ... catctcatagCATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 31

GAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACACCAATTACAGGAGGTGATGgtaagtatcg ... catctcatagCATTCATTTATGGTCACTCTGTTCGAAGCACTGTGGGAATGTCAAACATCCGTAGGATGATCGGAGTCTGCCCACAG