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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag

Basic information

species Zea mays
transcript GRMZM2G062034_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g13580.1 (Oryza sativa), 5'ss of exon 12
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgta---tgaagct----atcagaac---cgaaatatttttttaaatatgttt------agattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 ||||| || || | |||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||| | || ||||||   |||||||       | |||    |   | ||| ||| | | ||  |      ||||| || |||  |  |  || | |||||||  |  |||||| || |||| |||||
CTTCAAGGACATACAGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTCTGCATTTTCGCATATGGGCAAACTGGATCAGGAAAAACATACACTATGgtacgctgaagctcagggcaaaaacatttggtctgtttatttcagtttgcgtgccagaagatttctctacagtc-actatgtgtttacaacgatctgtttctatcaatttctcag

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 12
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 | |   || ||||   |  | || ||||||||||| ||||| || ||||| || || ||||| ||||| |||||||| ||||| |||||  ||||||||||||||| |  || |||   ||||   ||||||  |     || ||    |||   || ||||  | || |   ||     |  |||    || |||||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACAATGgtatgaa-ccctctgaat--aaattgatttttatct---catacatcatgttat--tgaaggaattcttcattctataagatgccaacc--tttctcag

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 14
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagc-tatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 ||||| || | ||  ||| | ||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||||| || ||||| ||| |||| |||||||| |   |||| |     |    |||| |      | | |||  |  |||||  | |    |   |||  | ||                       
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATATACGATGgtatgcattatatccgt-ttaatgctttttatgttgcgtatctagcctaatttact-tagcaactgcttttctactag----------------------

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 14
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagc-tatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 ||||| || | ||  ||| | ||| |||| ||||||||||| ||||||||||| || ||||| ||||||||||| || || ||||| ||| |||| |||||||| |   |||  |        | |||| |      | | | |  |  |||||  | |    |   |||  | ||                       
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATATACGATGgtatgcattatattcgtttaatgcttttttatgttgcgtatcttgtctaatttact-tagcaattgcttttctactag----------------------

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G04580.1 (Glycine max), 5'ss of exon 6
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 | |   || ||||   |  | || ||||||||||| ||||| || ||||| || || ||||| ||||| |||||||| ||||| |||||  |||| |||||||||| |  || |||     |||||  |||  ||    | | |   | |     || ||||  | || |   ||     |  |||    || |||||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACGATGgtatgaa-ccctctgaat----atattgatttttat---ctcatacatcatgctattgaaggaattcttcattctataagatgccaact--tttctcag

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
--TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatt---tttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
  |||||  |||||    || || ||| ||||||||||||| || |||||||| || || |||||||||||||| || |||||||| |||||  | |||||||||   |   |  || |    |  |||   |    | | |  |   ||| ||  |||  |     |||   |||  ||   || | || |            
ATTTTCA--GATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactcattcactagtatatcacgattaagtggccagacaaat---gatgccactacatt----cataccattatcattgtttttgtccag-----------

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 5'ss of exon 13
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggag--gatatatttacaataacttgtttcaatgaattgctcag
 ||    || ||  | || ||  |||| ||||| |||||||| ||||||||||| || ||||||||||| || || |||||||| |||||  ||||||||||||| |   |            | ||| |   | ||     ||||| | |    ||   |  |||    ||  |     | ||| |  |   |   ||||
CTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTATACAATGgtatgtattcactgt--------tgtttctgagagta-----agatttcataggaataacgctgatgcgcttttacc--ttcgttccctt---tctttcag

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 14
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
||||   |||| ||| ||| ||||| ||||  ||||||||||||| |||||||| || ||||| |||||||| ||||| || ||||||||  |||||||||||       || | || |   || || ||    ||||| ||  |  |  | |  ||  | | | |  | ||| |  ||  |||  |   |  |     
TTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTATACAATGgtaa------attacaagcttgattttgttaacgatatgctttaac-caatgattat--aagtttttctaacagtttctattttgcaaacacag-----

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 13
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 ||    || | ||  ||  |  |  |||| |||||||||||||| ||||| || || ||||| |||||||||||||| || || || ||| | |||||||||||||  | |         | |  |   |   |||||| | |||   || |  |   |  |  | | ||   ||   | ||||    |         
GTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATACACAATGgtatgaacttgtatatgttttagt-ctacatggcatatgtgttgatattttcaata---aaaacttgtgtaatgtattgtctttcctctag--------

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 15
-TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 |||  | || | ||  ||| ||||| |||| || |||||||| |||||||| || || ||||| |||||||||||||| || ||||||||  |||| |||||||| | | |            |||||||      ||    | | |   |||    |     ||| | |||   |   |||| |  |   ||   |||
ATTTTTA-GACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTATACTATGgtatgtacccactt---------tatttttc-----atccaaaaaatatgttaaagagattactatttgtacttcacactgttccttttgtttctccag

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ12333 (Selaginella moellendorffii), 5'ss of exon 9
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 |||   |||| || |||| | ||  | |||||||||||||| ||||| || || |||||||| ||||||||||| || || ||||||||  | || |||||||     ||| |    |  | |||      | || | |||  |    ||| |  |  ||                                      
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtat----ttatga----catattatacaacaacat-tatttgcaactatttgctgtacag--------------------------------------

upper sequence: GRMZM2G062034_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ19920 (Selaginella moellendorffii), 5'ss of exon 9
TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagctatcagaaccgaaatatttttttaaatatgtttagattcctttacgatggaggatatatttacaataacttgtttcaatgaattgctcag
 |||   |||| || |||| | ||  | |||||||||||||| ||||| || || |||||||| ||||||||||| || || ||||||||  | || |||||||       | |  ||  || |||      | || | |||  |    ||| |  |  ||                                      
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtat-------ttatgacataattatacaacaacat-tatttgcaactatttgctgtacag--------------------------------------

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: 22

TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagct ... aattgctcagATGGGTCCGGAAAACGCAACTGAGAAAGAATGGGGTGTCAACTATCGAGCACTAAATGACCTTTTCAACATCTCACATGATCGTCGGGACACAATTAAAT


Block sizes: 23 (upstream exon), 45 (downstream exon)
Score: 5

TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagct ... aattgctcagATGGGTCCGGAAAACGCAACTGAGAAAGAATGGGGTGTCAACTATCGAGCACTAAATGACCTTTTCAACATCTCACATGATCGTCGGGACACAATTAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagct ... aattgctcagATGGGTCCGGAAAACGCAACTGAGAAAGAATGGGGTGTCAACTATCGAGCACTAAATGACCTTTTCAACATCTCACATGATCGTCGGGACACAATTAAAT


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 19

TTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACATACAATGgtatgaagct ... aattgctcagATGGGTCCGGAAAACGCAACTGAGAAAGAATGGGGTGTCAACTATCGAGCACTAAATGACCTTTTCAACATCTCACATGATCGTCGGGACACAATTAAAT