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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgctttacagatttgttttacttgactgcttcctttaaagcttctgttgctttcggctatgcggatttgcaaagcaatttgctgccaattttattat...

Basic information

species Zea mays
transcript GRMZM2G097605_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097605_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 5'ss of exon 10
GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgctttacag-atttgttttactt-gactgcttcctttaaagcttctgttgctttcggctatgcggatttgcaaagcaatttgctgccaattttattat-
 |||||||||||||| ||  |||||||||||||||| || || || |||||||||||||||||||||||||||||||||||| | |||||||||||||||||||| |  | |  |||| |||| ||| ||||| | | | |  || ||   ||||||   |   ||   | ||| ||  || ||      ||| |||||    
CCATGATAAACGGTCTAAACTGCCTGGGTGGATACTGTCACACTTACATGATGCGCACCTAAATCTGAGCACTGATATGGCTTTGCATATAGCTCGTGAGgtatgttccataacatttatttttctttgactggtgc-tatgtagtttgaattgcttcaagtactgta-acttgtaat-catttaaagagcaagtttatctct

upper sequence: GRMZM2G097605_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G28290.1 (Glycine max), 5'ss of exon 11
GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgctttacagatttgttttacttgactgcttcctttaaagcttctgttgctttcggctatgcggatttgcaaagcaatttgctgccaattttattat--------
 ||||| ||||| || || |||||| | |||||||| || || || |||||||| ||||| ||  ||||||| || |||||| | |||||||| ||||||||||||  |     |||| |||| ||  |   || ||||  | | ||| || || | |  |||       | || |  ||||      | |||||||  |        
CCATGACAAACGTTCAAAATTGCCTAGTTGGATACTATCTCACTTACATGATGCCCACCTGAACTTGAGCACAGACATGGCTTTGCATATAGCACGTGAGgtatgccct-----tttgctttattttgc-attttctttttatcctctttttctgttgtttatttc--ccttcagataaattatgcttctattttatcttaagcagta

upper sequence: GRMZM2G097605_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 5'ss of exon 11
GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgctttacagatttgttttacttgactgcttcctttaaagcttctgttgctttcggctatgcggatttgcaaagcaatttgctgccaattttattat--
 |||||||| ||||||||  | ||||| |||||||| |||||| ||| |||||| ||| | ||||| ||||||||||||||| | || || ||||| ||||||  | | | |  |   |  |  || |   ||  |  | || |             |||     | ||   |||      | | |     |||| ||    
TCATGATAAGCGGTCCAAACTACCTGGTTGGATACTTTCGCATCTGCGTGATGCACACTTGAATCTAAGCACTGATATGGCTATTCACATTGCTCGAGAGgtaaacct-ataactcgctgcttttttataactcacagtgaaacaaacaaca----aggcataaagaatcaacaattttcctggtttttgttttttttgcag

upper sequence: GRMZM2G097605_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 5'ss of exon 11
GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgctttacagatttgttttacttgactgcttcctttaaagcttctgttgctttcggctatgcggatttgcaaagcaatttgctgccaattttattat---
 ||||||||||| || || |||||||||||||| || || ||||| | |||||| ||||| ||| |||||||||| |||||| | ||||| || || ||||||||  |   |       |  ||     || |    || |  | |  |      |  | ||  | |     |     | | || |  ||||   |  ||   
TCATGATAAACGCTCTAAATTGCCTGGGTGGATTCTGTCACATTTACGTGATGCACACCTGAATTTGAGCACTGACATGGCTTTGCATATTGCACGAGAGgtatgtctcttattgcgtgtccacaatcttgatattattga--ccttggaaaacatgagataatctgtcagacttgaaagtatggt-tcaataggagcatgtc

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|33093450|gb|CF053444.1|CF053444
EST:     ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
EST: gi|211462979|gb|FL459139.1|FL459139
EST:     ATGCGCACCTAAATYTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
EST: gi|37383190|gb|CF628585.1|CF628585
EST:     ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
EST: gi|71429989|gb|DR811039.1|DR811039
EST:     ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTTTCCGGAGGATGGCACAGCCATATGCCAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
EST: gi|86467670|gb|DY234040.1|DY234040
EST:     ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
EST: gi|61118799|gb|DN559760.1|DN559760
EST:     ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAG                         TTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG
genomic: ATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 84

GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAGAAAACGCTGTTAACCGAGGAGGATCTGGAGAATTTGGCGCAGGATGGCA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 75

GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAGAAAACGCTGTTAACCGAGGAGGATCTGGAGAATTTGGCGCAGGATGGCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 44

GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAGAAAACGCTGTTAACCGAGGAGGATCTGGAGAATTTGGCGCAGGATGGCA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 39

GCATGATAAACGGTCCAAGTTGCCTGGGTGGATACTCTCGCATTTGCATGATGCGCACCTAAATCTGAGCACTGATATGGCTCTCCATATAGCTCGTGAGgtatgcttta ... tctgcaacagTTTCTCCGGAGGATGGCACAGCCATATGACAAGGCGGGAAGCGGTGGCAAGAAAACGCTGTTAACCGAGGAGGATCTGGAGAATTTGGCGCAGGATGGCA