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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaactgcctggtgcctgcatcatggccagttaattattgccagcattaaaagtactatgttaacattatttcttgtttattttttcag

Basic information

species Zea mays
transcript GRMZM2G159002_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159002_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G04810.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaactgcctggtgcctgcatcatggccagttaattattgccagcattaaaagtactatgttaacattatttc--ttgtttattttttcag-------
|  |||||||| ||||| || ||| |  |||| ||||| ||||| |||||| ||||||||||||| || || || |||||||||  ||| || ||  || || ||||  |    | |  || | |  |   |   || || ||     || |      ||   ||  ||| ||  ||  || |   | ||   ||       
TATTACTTGGGTGAGCTTAACGATTCCTTGTCCTATGCCCTTGGAGCTGGATCCTTGTTTGATGTGTCAGAGGATTCTGATTATATTCATACTCTTCTATgtaaggattttgaagtttgctactttcttctcttctactttttttatccaattctgtgac--agtagacactagctcggttatcattcttaataggcgtaaa

upper sequence: GRMZM2G159002_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G32730.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgagga-------actgcctggtgcctgcatcatggcca-gttaattattgccagcattaaaagtactatgttaacattatttcttgtttatttttt--cag
|  |||||||||||||| |||||| | ||||| ||||| || || || || ||||| ||||||||||| || || |||||||||| ||| || ||  | ||||||||         |   || ||  |  |   |   || | |  |   || | | |  |      ||| | ||||  | |||  ||   |||  ||  || 
TATTACTTGGGCGAGCTTAATGATTCGCTGTCTTATGCCCTAGGAGCCGGTCCCTTATTTGATGTTTCAGAGGATTCTGATTATGTTCATACGCTTCTGGgtgaggattgagaagtttgttgatgtttttactctcttcatgctgttctctgtctgtag-actctagctagggtaac--tgtttaatgcaaattgcttaccaa

upper sequence: GRMZM2G159002_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv10s0042g00800.t01 (Vitis vinifera), 5'ss of exon 3
TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgag---gaactgcctggtgcctgcatcatggccagttaattattgccagcattaaaagtactatgttaacattatttcttgtttattttttcag---------
|  |||||||| || || |||||  |  |||| ||||||||||| ||||| ||||| ||||||||||| || || ||||||||||  || || ||  | ||| ||   ||  |||  | |||    ||  |   |||  | |||||      | || | |     | |||| | | |   |   ||||   ||||          
TATTACTTGGGTGAACTCAATGACTCATTGTCGTATGCACTTGGAGCTGGTCCCTTATTTGATGTTTCAGAGGATTCTGATTATGTCCACACTCTTCTTGgtaagaatgatatgcacgttgcactgatttta-tcaggaagttattatacttactacagg----gttttaaaactttgcatgtgttataacttcaattacctatg

upper sequence: GRMZM2G159002_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv00s0215g00040.t01 (Vitis vinifera), 5'ss of exon 3
TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaactgcctggtgc-ctgcatcatggccagttaattattgccagcattaaaagtactatgttaaca-ttatttcttgtttattttttcag-------
|  ||| | |||||||| |||||  |  |||| || |||||||| ||||| ||||| ||||||||||| || || ||||||||||  || || ||  | ||| || |  ||  |||     ||||       ||        |   ||  |||  | ||  | |     || |||    |    |   | |  |        
TATTACCTAGGCGAGCTCAATGACTCGTTGTCGTACGCACTTGGAGCTGGTCCCTTATTTGATGTTTCAGAGGATTCTGATTATGTACACACTCTTCTTGgtaagaa--tgattggcatgttgcactgatttcatcagggagtcatcataattgcatgtggtttaactccaattaccaatgaaatggatgtaaatgggagtt

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|148944688|gb|EC889825.2|EC889825
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|149078849|gb|EE167663.2|EE167663
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|78083538|gb|DV511931.1|DV511931
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|148946605|gb|EC891864.2|EC891864
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|149014543|gb|EE044180.2|EE044180
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|71449454|gb|DR830504.1|DR830504
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
EST: gi|148938539|gb|EC882859.2|EC882859
EST:     ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAG                         CAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG
genomic: ACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 235

TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAGAAAAAACGATCGACCCTAGGCTGGAGGCCATAGTGGAAAGGATGCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAGAAAAAACGATCGACCCTAGGCTGGAGGCCATAGTGGAAAGGATGCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAGAAAAAACGATCGACCCTAGGCTGGAGGCCATAGTGGAAAGGATGCTGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

TTCTACTTGGGCGAGCTAAATGATGCTCTGTCATATGCACTTGGCGCTGGACCCTTGTTTGATGTTTCTGACGACTCTGATTATGCTCAAACACTGTTAGgtgaggaact ... attttttcagCAAAAGCTTTGGATGAATATACTGCCATCCAATCAAGGGGCACTGGGGAAGAAAAAACGATCGACCCTAGGCTGGAGGCCATAGTGGAAAGGATGCTGGA