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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgcttatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaatcgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag

Basic information

species Zea mays
transcript GRMZM2G481548_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G481548_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g72980.2 (Oryza sativa), 5'ss of exon 11
ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaatt-gcttatggggttatgcga--tagtgtta-----tggagtagatttacgatggaagct----gaactgctagaacaatggtacatgaatcgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag
||  ||||||||| |||| |||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||||| || ||||||||||| || ||||||||| ||||   || | ||| |   | ||  ||     |    |  | |||  | ||| |||    ||||||  |||| ||  || ||| || | ||                                                                                                              
ATATGGAAATGAACATTTGTCTCGAATTGAGAAAGAATGTGTGGAGATTGATATTAAGTACGAAGGTTTTATAGCACGGCAGCAAAGTCAATTGCAGCAGgtaatttgctttgtggatcatgtgcatttgtcctacttcctaagatgcacttataagggaggctctttgaactgaaagaaaaaatgtgcataaa-cattta------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G481548_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G00380.1 (Glycine max), 5'ss of exon 10
ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgcttatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaatcgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag
 | |||  |  |||  |||||  |||| ||||| |||||||| ||||||||||| ||||||||||||||||||   || || ||||| ||| | || |||||| ||| |          |  |  | ||  |   |||  || |    |    ||||       |  ||||     | | |||| |        |  ||   |  |||||| |  |  ||||||        |||||    ||| || || |   |  | || | | ||||| ||   | |||  || |        
TTTCGGTGACAAAAGCTTATCAAGAATGGAGAAAGAATGTGTTGAGATTGATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgtt------acactttgtcaatgagaaaaagtgaatctgtttt---tgctgtgtcaacatgacaac----cctaaatcat--------tttaatttttacacatttt--agcatttca--------gttttcagctgtgtatttaacgtgaaatctcattgttgtgatg---gatttacctatag------

upper sequence: GRMZM2G481548_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G32720.1 (Glycine max), 5'ss of exon 8
ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgct-tatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaat-cgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag
 | |||  |  |||  |||||  |||| ||||| |||||||| ||||||||||| ||||||||||||||||||   || || ||||| ||| | || |||||| ||| |  |   |   ||| |  |  || |  |  |   |      |  |      |   ||| | || |   |  |  |  | ||  |||  | || |  | | |  | |      || ||||| ||| || |   |||   |  |                                                 
TTTCGGCGACAAAAGCTTATCAAGAATGGAGAAAGAATGTGTCGAGATTGATATAAAGTATGAAGGTTTCATCTTGCGTCAGCAAAGCCAACTTCAACAGgtatttgttacacttgtcaatgaggaaaagtgaatgtttttttgctgtgtcaacatcacaaccctaaatcattttaatttttacacattttagaatttcagct-tggtatttaacttgaaatctcatt-gttgtgatggatttacctatag------------------------------------------------

upper sequence: GRMZM2G481548_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 5'ss of exon 11
ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgcttatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaatcgttcgagatgtccaacagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag
 |  ||||||||||  |||||| |||| ||||| || ||||||||||| ||||| || |||||||||||||| |  || || ||||  ||| | || ||||||  |     || | |      ||      ||  | ||    |||  ||    ||    |    | |||  |    || | |  |     ||    || ||                                                                                               
CTTTGGAAATGAAACATTATCTAGAATGGAGAAAGACTGTGTAGAGATCGATATAAAATATGAAGGTTTCATTGTTCGCCAGCAAAACCAACTGCAGCAGgtatct-----tgtgttagcttcattactccattaaata---ctact-tgcttactcggatatatggacatggagttataagttat-----atccttaatag-----------------------------------------------------------------------------------------------

upper sequence: GRMZM2G481548_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0044g01690.t01 (Vitis vinifera), 5'ss of exon 11
ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgct---tatggggttatgcgatagtgttatggagtagatttacgatggaagctgaactgctagaacaatggtacatgaatcgttcgagatgtccaa-cagtagcacattatgcatgatttcatttgttttgttttgttttgtttaattgataaggcagctaacttttgtgttgtttgttttctctctttgttaag
 |  |||||||||  | | ||   ||| ||||| |||||||| |||||||||||||||||||| || || ||    || || || || ||  | || ||||| | || |   |||  ||| |    || |  ||         |||||  ||  ||  ||   ||    ||     |  |||  |    ||    |||  || | ||   | ||| | | | |||  ||||||                                                                    
TTTTGGAAATGAACTTCTGTCCAAAATAGAGAAAGAATGTGTGGAGATTGATATCAAGTATGAGGGCTTTATTATGCGGCAGCAGAGCCAGCTCCAACAGgtgaatgatccatatttggtcactt-attgcctttcatttcctatttagaat--aatttgtcatgtctaaatttctgggcatatacttgtc----tgtttaatccgtcatagatttttccttattgtatttgtag------------------------------------------------------------------

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|76017300|gb|DT944470.1|DT944470
EST:     ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAG                         ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
genomic: ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
EST: gi|83279108|gb|DV943116.1|DV943116
EST:     AACAAAGTCAATTACATCAG                         ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
genomic: AACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
EST: gi|32864358|gb|CF004040.1|CF004040
EST:     ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAG                         ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
genomic: ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
EST: gi|71329102|gb|DR801260.1|DR801260
EST:     ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAG                         ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
genomic: ATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
EST: gi|16925054|gb|BM078122.1|BM078122
EST:     CGCACGACAACAAAGTCAATTACATCAG                         ATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA
genomic: CGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCA

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: 42 (upstream exon), 49 (downstream exon)
Score: 23

ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 52

ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 29

ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 29

ATGCGGAAATGAAAATTTATCTCGAATTGAGAAGGAATGTGTAGAGATTGATATCAAGTATGAAGGTTTCATCGCACGACAACAAAGTCAATTACATCAGgtaattgctt ... ctttgttaagATCGTAAACCAAGAACACAGGAAACTTCCTGAAGATTTGGATTACCACTCAATGACAAATCTATCACTTGAAGCTCGTGAGAAACTTTCCAAG