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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttggaagttggaagattactgaatctttgcttctttcagattccatttatgttcatcctatcatcatcacctagtgtggtaccagtcttgctgca...

Basic information

species Zea mays
transcript GRMZM2G125243_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125243_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 5'ss of exon 6
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgta-atttggaagttggaagattactgaatctttgcttctttcagatt-ccatttatgttcatcctatcatcatcacctagtgtggtaccagtcttgctgca
|||||||| || ||||||||||||||||||||||| ||||||||||| ||| |||| |||||   |||| || || | |   |  ||||   ||  || | | | |||    || |  || | | | |  | | |  |   | |  |  |  || |  |   
ACACTTCGCCGCCTTGCCCAAAATCGTGAAGCTGCTAGGAAAAGCCGTTTAAGAAAGAAGgtgtgtttgtaactttgtatgatcttgaaatgtt--ttatctgatattgttgttgaatttgaacttctactgagctacatatatattttctttcatcatctc

upper sequence: GRMZM2G125243_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 7
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaa----------------tttggaag---ttggaagattactgaatctttgcttctttcag-attccatttatgttcatccta----tcatcatcacctagtgtggtaccagtcttgctgca----------------------------------
||| |  | || ||||| ||||||||||| |||||||||||||||||| |  | ||||||||||                ||| || |   |||||| |||| ||     |  |||  ||     ||| || | |  |  |  |      || || |   |  |||  ||  | | || ||| |                                  
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttctgttaattttagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttatcatgttttataaatatttctgaacttcttttttaaatccttgtttctattcattcag

upper sequence: GRMZM2G125243_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G31050.3 (Glycine max), 5'ss of exon 7
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaa---------tttggaagttggaagattactgaatctttgcttctttcagattccatttatgttcatcctatcatcatc---acctagtgtggtaccagtcttgctgca--------------------------------------------
||| |  | || ||||| ||||||||||| |||||||||||||||||| |  | ||||||||||           |  |  || || ||      ||  ||    |  |  || ||   ||  ||||||   | |||| ||    ||| | |    |  ||   ||  |  |                                            
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttccgttaattttagatgaacttgtaaaattattgtgatataggttggtttgttgttcaatatgtcattattgagacccaataatttgtcatgttttatatatattttttgacttattttttaaatccctctttctattcattcag

upper sequence: GRMZM2G125243_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 2
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaa-------tttg------------gaagttggaagattactgaatctttgcttctttcag-attccatttatgttcatccta----tcatcatcacctagtgtggtaccagtcttgctgca----------------------------------
||| |  | || ||||| ||||||||||| |||||||||||||||||| |  | |||| |||||       | ||            ||| |||||| |||| ||     |  |||  ||     ||| || | |  |  |  |      || || |   |  |||  ||  | | || ||| |                                  
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATGgtaaggccttttctgttaattgtagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttgtcatgttttataaatatttctgaacttcttttttaaatccttgtttctatttattcag

upper sequence: GRMZM2G125243_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 6
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttggaagttggaa-gattactgaatctttgcttctttcagattccat-ttatgttcatcctatcatcatcacctagtgt--ggtaccagtcttgctgca----------------------------------------------------------------------------------------------
||| | || || ||||| |||||||||||||||||||| |||||||||||| | |||||||||  |       || || || | |  | |   ||      |||  |||  | |||||||    | | |    |  |  |||||  | ||      ||  ||                                                                                                
ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgtt-gcacaaactgagtttctaagtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttag

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|211164173|gb|FL132748.1|FL132748
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164177|gb|FL132752.1|FL132752
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164169|gb|FL132744.1|FL132744
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164175|gb|FL132750.1|FL132750
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164176|gb|FL132751.1|FL132751
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|18660490|gb|BM500889.1|BM500889
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164172|gb|FL132747.1|FL132747
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164171|gb|FL132746.1|FL132746
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164170|gb|FL132745.1|FL132745
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCWTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
EST: gi|211164174|gb|FL132749.1|FL132749
EST:     GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGTTTACGAAAAAAG                         GCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG
genomic: GTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAG

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: 43 (upstream exon), 46 (downstream exon)
Score: 32

ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 59

ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 115

ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 7

ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttgga ... ttttcttcagGCATACATCCAAAACCTTGAGAGTAGCAGACTGAAACTTACTCAGTTAGAGCAAGAGCTTCAGCGGGCTCGTCAACAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTTCGGCGTCTTGCCCAAAATCGTGAAGCTGCCAGGAAAAGCCGATTACGAAAAAAGgtaatttggaagttggaagattactgaatctttgcttctttcagattccatttatgttcatcctatcatcatcacctagtgtggtaccagtcttgctgca

- - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - -  AGCTGC