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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 10
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgt--attctaaagtttcg--aggcaatagttcataatgcatctgatcctgttatatcatc-tataactgatagaataaccatgttttttag
| | ||||| |||||||||||||| ||||||||||| |||||||||||||||||| |||| |||||||| |||||||||||||| |||||||| ||||||||   || ||||  |     ||| |||| |||||| |   | |   | ||| | || | | | | |    |||                  
ACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAATGAGAGTCGCTGGTGTTCTTCATATCTTTCAGTTTGAAACTAAGCAGgttagttttaaatctctaccaggaaataattcatactatgtgtaggc-tgtgaaataaccatctgatatttag------------------

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 12
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaat-----------agttcataat----gcatctgatcctgtt-atatcatctataactgatagaataaccatgtttt-ttag--------------------
 || || ||||| ||||||||||| |||||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||| ||||||||||||||||||||   | | |  | | || |           | ||| ||||    || | ||  | | || ||||| ||  ||  |  | || | |   | | || ||||                    
GTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAGgtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactt--tggagttattttatattattagtattttatcattctttgaag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA16G21340.1 (Glycine max), 5'ss of exon 15
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag
 || |||||||| ||||||||||| |||||||||||||| || || ||||||||||||||||| ||||| || || || || || |||||||| ||||||||||  ||    || |  |   | |  || | |   | ||    | || | |||      |||| ||   || |  |   || |||
GTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataata--cctttgttgatgttgcacaaactttctttggaattattttgtcac-----actggtattttatctcttggttgtag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA09G32740.1 (Glycine max), 5'ss of exon 12
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgttatatcatcta---taactgatagaataaccatgttttttag
 || |||||||| ||||||||||| ||||| |||||||| || |||||||||||||||||||| ||||| || || || || || |||||||| ||||||||||  ||   |||   |   ||    || ||  |   || | || |   || || |    | |||||||   || | || | || |||
GTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAATGCGAGTTGCAGGTGTTCTCCACATATTCCAGTTTGAAACCAAGCAGgtataatacc-tttgttgatgatgtcacacaa-acccttgtttctttggaattattttgcctcactgatattttatctatttgttgtag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 12
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaat-----------agttcataat----gcatctgatcctg--ttatatcatctataactgatagaataaccatgttttttag---------------------
||| |||||||| ||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||| ||||| || || || ||||||||||||||||||||   | |||  | | || |           ||||| ||||     | | ||  | ||  | ||||| ||  ||  |  |  | | |   | |||| | |                     
ATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGGGTTGCAGGTGTTCTTCACATATTCCAGTTTGAAACAAAGCAGgtattggcatgttcagggacactgtactcttcctagttcttaatttcgacctttggacttgactcatatcttcattactt--tgaagttattttattttattggtattttatcattctttgaag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 5'ss of exon 9
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaa--agtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag
| || | ||||||||||||||||| ||||| || |||||||| || || |||||| |||| |||||||| ||||| || ||||| || || ||||| ||||| |    |  | | |    | |  | |  || ||| | |   ||||  |||   || |  || |     ||     |||||| |   
ACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAATGAGAGTCGCTGGTGTTCTTCACATATTTCAGTTCGAGACAAAACAGgtttaaacatcactatttgtggatcattatattatgaagcaattcct--tatgagatattcaatttgggtaacttgtatgtttgtag-

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 11
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattcta------aagtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag--------------------------------------------
| ||||||| || ||||||||||||||||||||||||||||| || ||||| ||| ||||||| |||||||| || || || || |||||||| || |||||  |  |       |||||| |        |  ||||    | |     | |  | || | | |   | ||  | |  || |||||                                                 
ACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtatt--ccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 5'ss of exon 13
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagt----tcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag--------------------
  |  | || ||||||||||| || || || |||||||| ||||| ||||| ||||| |||||||| || |||||||| || || || |||||||||||||||||   || |   | |  | | ||    |||||    | ||| | | ||  | | ||   | | | |||   |    || | |  |                      
GCTGCGTGATATCATGCAATTCGGCAGTAGTAATACTGCCGTTTTTTTTAAGATGCGTGTTGCTGGAGTTCTTCATATTTTCCAGTTCGAAACAAAGCAGgtatttataaatcaagtgtaagtcgtacggtcatatccaagctgctgcggtggttttatgagtcatttataacttggtaatttatgatgtgtgggattggcttcaaacag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgt-tatatcatctataactgatagaataaccatgttttttag----------------
 ||  |||| |||||||| ||||| || || || |||||||| || |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||||||||     | | |  | |     | ||||| |  | ||  | | || |  ||    | | | | ||     ||| || |  | ||                 
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatct---attcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S364_50V6.1 (Physcomitrella patens), 5'ss of exon 13
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag----
| |  | ||||| |||||||||||||||||||| || || || || || |||||||| || || ||||| || ||||| ||||| ||||| || |||||||| |  |   ||  | ||    |  ||  || |    |  ||||   ||||| || |   |    ||   |     ||| || |      
ACTGCGCGACATTATGCAATTTGGTAGCAGCAACACAGCCGTCTTTTTCAAAATGCGTGTAGCGGGTGTACTGCATATTTTTCAGTTTGAGACTAAGCAGgt-tattttcgtacctagatcttgctttgtactt--gcaaatccc--tatattattttggagatttatttttggtttgtcttgtgagcag

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ30174 (Selaginella moellendorffii), 5'ss of exon 11
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaag--tttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag
  | |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||  | || || ||||| |||||||| || ||||| |  |   |  ||||   | | |  |||   |    ||||   | |                                        
GCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtctttgtggctttccgtgtagttcttctctaaatttctgtcgcag----------------------------------------

upper sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
lower sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaag--tttcgaggcaatagttcataatgcatctgatcctgttatatcatctataactgatagaataaccatgttttttag
  | |||||||||||||||||||| || |||||||| || || || ||||||||||| || || || ||  | || || ||||| |||||||| || ||||| || |   |  ||||   | | |  |||   |    ||||   | |                                        
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtttttgtggctttccgtgtagttcttctctaaatttctgtcgcag----------------------------------------

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|211028431|gb|FL442904.1|FL442904
EST:     AATGCGAGTGGCTGGTGTCCTTCCATATCTTTCAATTTGAAACAAAGCAGG                         GGCGAGGGAAATATGTGTAGCAC-TCAAACACCATATAAATGACGTCATG
genomic: AATGCGAGTTGCTGGTGTCCTT-CATATCTTTCAATTTGAAACAAAGCA-Ggtattctaaa ... tgttttttagGGCGA-GGAAATATGTGTAGCACTTCAAACA-CATATAAATGACGTCATG
EST: gi|18383721|gb|BM416921.1|BM416921
EST:     AAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAG                         GGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTC
genomic: AAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTC
EST: gi|18649769|gb|BM498588.1|BM498588
EST:     AAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAG                         GGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTC
genomic: AAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTC

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: 184

ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 25

ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaa ... tgttttttagGGCGAGGAAATATGTGTAGCACTTCAAACACATATAAATGACGTCATGCTCCGCAGATATTCAAAAGCACGCTCTGCTAATAGTGTGACATCGCAAAATG