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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctctgtccacattgaatgctctggttatttggaagttggatctctgctcacctgctgccacctgttttgcag

Basic information

species Zea mays
transcript GRMZM2G438895_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g50370.1 (Oryza sativa), 5'ss of exon 7
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctctgtccacattgaatgctctggttatttggaagttggatctct-gctcacctgctgccacctgtt-ttgcag-------------------
||||||||||||||| |||||||||||||||||| ||||||| ||||| ||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||  |||| |||     || | || |||||||||||||   | |||       |   | |||  | |  |||||                    
CAGGAAGGCAACCCTTTGTGTCCATCCAGATAAATTACAGCAAAGGGGTGCTACAATCAGACAGAAATACATATGCGAGAAGGTTTTTGATCTTCTTAAGgtttgtgcaatgtctacaaaatttgttatgattatttggaagttcattttctcatgtgtccttttccatttctgattgcattagtacaagcatgtttgca

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G25190.1 (Glycine max), 5'ss of exon 9
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgt---gctctgtccacattgaatgctctggttatttgga--agttggatctctgctcacctgct---gccacctgttttgcag-------------
||||||||| ||||| ||||||||||| || ||  |||||||  | || || |  ||   ||| ||||||||||||||||| || |||||||| || |||||||||   ||   |      |    |  | |  ||||||| |     || ||    |   |  |||    || | |  |  ||| |             
CAGGAAGGCCACCCTTTGTGTCCATCCTGACAAGTTACAGCAACGTGGAGCAAGTATTCAACACAAATACATATGTGAGAAAGTCTTTGATCTACTAAAGgtatgtcttgcatggcatctttcagttaatttatttatttgaaccgtctgcatagggggatatttgccagagcaaaccataatgctgttatctatcaagt

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G07550.1 (Glycine max), 5'ss of exon 12
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctctgtccacattgaatgctctggttatttggaa--gttggatctctgctcacctgctgccacc-tgttttgcag------------------
||||||||| ||||| ||||| ||||| || ||| |||||||  | || || |  ||   ||| |||||||||||||| |||||||| |||||| | |||||||||  |   | |   |   ||  |    ||| ||||    |||   | | |  |   ||||    |   |||  |  |                   
CAGGAAGGCCACCCTGTGTGTTCATCCTGACAAATTACAGCAACGTGGAGCAAGTATTCAACACAAATACATATGTGAAAAGGTTTTCGATCTTTTGAAGgtatgtaatgcatgctattgctatctttcacttagttggttttgttcattttttattttgctgcaaaaaaaatgtcctatacctagtatggataaggaat

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G25150.1 (Glycine max), 5'ss of exon 7
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgt---gctctgtccacattgaatgctctggttatttggaagttggatctctgctcacctgct---gccacctgttttgcag---------------
||||||||| ||||| ||||||||||| || ||  | |||||  | || || |  ||   ||| ||||||||||||||||| || |||||||| || |||||||||   ||   |      |    |  | |  ||||||| |   |     |  |   |  |||    || | |  |  ||| |               
CAGGAAGGCCACCCTTTGTGTCCATCCTGACAAGTTGCAGCAACGTGGAGCAAGTATTCAACACAAATACATATGTGAGAAAGTCTTTGATCTCCTAAAGgtatgtcttgcatggcatctttcagttaatttatttatttgaaccgtctgcatagggatatttgccagagcaaaccataatgctgttgcataacttaaaa

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G06160.1 (Glycine max), 5'ss of exon 14
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgt-------gctctgtccacattgaatgctctgg--ttatttg-gaagttggatctctgctcacctgctgccacc-tgttttgcag----------
 |||||||| ||||| ||||||||||| || ||  |||||||  | || || |  ||   | | |||||||||||||||||||| |||||||| || |||||||||       ||  | |     |||| |  | | |    || ||  |||  |||| | |     |   |    |   ||||    |           
TAGGAAGGCCACCCTTTGTGTCCATCCTGACAAGTTACAGCAACGCGGAGCGAGTATTCAAAACAAATACATATGTGAGAAGGTCTTTGATCTCCTAAAGgtatgtcatgcatgccatctttcagttgatttattttgaaccatctgcaaaggaggatttgtcagagcaaaccataataatgttgcataactaaaatcta

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G37760.1 (Glycine max), 5'ss of exon 7
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctctgtccacattgaatgctctggttatttggaagttggatctctgctcacctgctgccac----ctgttttgcag------------------
||||||||| ||||| ||||| ||||| || ||| |||||||  | || || |  ||   ||| |||||||||||||| |||||||| |||||| | |||||||||  |   | |  ||||    || |   | | | ||  ||     | |  |    || ||| |       ||  |  |                   
CAGGAAGGCCACCCTGTGTGTTCATCCTGACAAATTACAGCAACGTGGAGCAAGTATTCAACACAAATACATATGTGAAAAGGTTTTCGATCTTTTGAAGgtatgtaatgcttgc-tattgctatctttcactttgttgattttattcattttttattttgttgcaaaaaaatggtcctatacctagtatggataaggaat

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv18s0001g12770.t01 (Vitis vinifera), 5'ss of exon 6
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatg-tgctctgtccacat-tgaat--gctctggt-tatttggaagttggatctctgctcacctgctgccacctg---ttttgcag-------------
| ||||||| || || ||||| ||||| |||||  | |||||| | || ||||  ||    ||||| ||||||||||||||||||||||||||| |  ||||||| || | | | |   | || ||  |||   || | |||    | | |    |     | |||  |     |    ||||| ||             
CCGGAAGGCCACTCTTTGTGTGCATCCTGATAAGTTGCAGCAGCGTGGTGCTAGCATTCAGCAGAAGTACATATGTGAGAAGGTTTTTGATCTTTTACAGgtatgctgttgtcttcttttgtgcattagcttaagtatctttatgggctagtgagcactaaaactgaagaggtttcaatttttgtagtaatgcctaaata

upper sequence: GRMZM2G438895_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv04s0023g02070.t01 (Vitis vinifera), 5'ss of exon 7
CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctctgtc---cacattgaatgctctggttatttggaagttggatctctgct-cacctgctgccacctgttttgcag-----------------
 || || || || || ||||| ||||| || ||| |||| || ||||| || |  ||   |||||| ||||||||||| ||||||||||||||||| ||||| |||   | |||   ||  ||   | |     ||  ||     ||  || |||  | |     ||   | ||||||    |                 
TAGAAAAGCCACTCTTTGTGTTCATCCTGACAAATTACAACAAAGGGGTGCAAGCATTCAACAGAAGTACATATGTGAAAAGGTTTTTGATCTTCTAAAGgtgtgtcaccagtctgccattttctttcccaaaattgatttctgattaaatgtctaatacttacacttaaaactgtttccatgcctataggcctctaaac

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|4646794|gb|AI621869.1|AI621869
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG
EST: gi|113814220|gb|DW931581.1|DW931581
EST:     CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAG                         GATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG
genomic: CTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG

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), 46 (downstream exon)
Score: 146

CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 43

CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 37

CAGGAAGGCAACCCTATGTGTCCATCCAGATAAACTACAGCAGAGGGGCGCTACGATCAGACAGAAATACATATGTGAGAAGGTTTTTGATCTTCTTAAGgtatgtgctc ... tgttttgcagGATGCTTGGAACAAATTCACTTCGGAGGAGCGCTAG