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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg...

Basic information

species Zea mays
transcript GRMZM5G813143_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaa-tgaaatttacactatcgtaataattttctaca----gtaatgttattgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg-----------
||||||||| |||||||| ||||||||||||||| |||||||||||||||||||||||||||| |||||| |  |  | ||||| || |||    ||||||| | ||||| ||||||   ||||  | |||||||    | | | |   | |     | | || || |  || ||       ||   ||   |     | ||           
GGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGgtaaaattaaattcacactactataatcttcttctacacagggaagtttgggtatagtcttctattctgcagttgagtacatcctataacttagtatcttctttgctacttcacag

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G40860.1 (Glycine max), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataatttt-ctaca-gtaatgttattgttagactatgttgtgtatgtgtgtgtggaacat-ggtttttaaaacggtatg
||| |||||||||||||| || |||||||| || ||||| |||||||| ||||  ||||  | || ||| |||  ||| ||  || | ||     ||||| ||   ||||  |  ||    |||||| | || ||    |||  |||||| ||  |||     |       |    |  ||   || | ||    |  | 
GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGgtatatagcattt-tagcatgtacataattctgctgcataccatggaattgtt-gataatgacaaattatcaaatagcaatgatcaattctcaatcttgagt-

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G43360.1 (Glycine max), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg
||||||||| |||||||| || ||||||||||| ||||| || ||||| |||| |||||  | || | | |||  |||  || |||  ||     ||||  || | ||||| | ||    ||||||     | | || || |    |  ||  || |  || |  |||||    | ||                   
GGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAACTGTGTCAACAGTTAGCTCCCTGgt--ataatattta-attagta-aataataaa--ataatattgatcaactctgatcatttgctgca-atgtgttcatatcag------------------

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G40880.3 (Glycine max), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaaca-tggtttttaaaacggtatg
 |||||||| |||||||| || ||||||||||| ||||| || ||||| |||| |||||  | || | | |||  | | ||  ||   |   |  ||||| |  |  ||  ||||  |       | || ||  |||   || ||    |   |   |  | |  |    |   |  |    |   |    |    ||
AGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGGTGGCAAAGGAGTTCTGGAAAATATGCCTGCAAGTACAGTCCTGgtacaatattttagcactgactctgct-tcttatattgtagaatttttccatgtgaaaaattaggagataatagcaaattaacaatccatccttcatcttg

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgtt-attgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg
||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||| ||||| ||| |  |||||| || | ||  || | ||| |  ||||  ||| | || |  || || |  | |             |||| ||||||  ||||   | | | |      |                          
GGAACTTGGAATTGGAATAGTACCATACAGCCCCCTTGGCCGTGGATTTTTTGGTGGCAAGGCTGTCGTAGAAAGTATACCTGCAAACAGTTTTCTGgt--atggacttaaacctttctttctgacaacacttgcccttgttcattgttc-actaacatctctttccaccag--------------------------

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G27130.1 (Glycine max), 5'ss of exon 6
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg
||||||||| |||||||| || ||||||||||| ||||| || ||||| |||| |||||  | || | | |||  |||  || |||  ||                                                                                                           
GGAGCTTGGCATTGGAATTGTACCATATAGCCCTCTTGGTCGAGGCTTTTTTGgtggcaaaggagttctggaaactgtgtcaacagttag-----------------------------------------------------------------------------------------------------------

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0020g04130.t01 (Vitis vinifera), 5'ss of exon 5
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaa-atttacactatcgtaataattttc-tacagtaatgttattgttagactatgttgtgtat------gtgtgtgtggaacatgg----tttttaaaacggtatg--------------------------------------
 ||||||||||||||||||||  |||||||||| ||||| ||||| ||||||| ||| | ||||| ||| ||  |  | ||  |  | ||| |  |||| | | |  ||  | |  |   || ||||||   || ||     |    ||  || | | || |   |       || |    |||||| |    |||||  | |  |                                         
AGAGCTTGGTATTGGAATAGTAGCATATAGCCCTCTTGGTCGTGGATTCTTTGGTGGGAAGGCAGTTGTGGAGAGCTTGCCCACTCAGAGTATCCTGgtcagtaactatagataaaaatttagtaatttgaatataggttcttctccgtctgagttttttttacttcttttgatgggcaaagaacatcgatcatttttttagcattggaatcagttatttaaattcatactgacattcctgccacag

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|91877298|gb|EB407255.1|EB407255
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76292810|gb|DV032378.1|DV032378
EST:     TGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|78105722|gb|DV524140.1|DV524140
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76021183|gb|DT948353.1|DT948353
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91875442|gb|EB405399.1|EB405399
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTAGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|78114482|gb|DV532871.1|DV532871
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|89761100|gb|DY689250.1|DY689250
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTTTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76288051|gb|DV027619.1|DV027619
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|101392432|gb|EB818145.1|EB818145
EST:     TCTTTGTTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAGGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|89755224|gb|DY685733.1|DY685733
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|76011255|gb|DT938425.1|DT938425
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|60355056|gb|DN222029.1|DN222029
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|91873436|gb|EB403393.1|EB403393
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|78112031|gb|DV530427.1|DV530427
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
EST: gi|60341512|gb|DN208485.1|DN208485
EST:     TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG                         TCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG
genomic: TCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTG

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: 81

GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 56

GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 89

GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 19

GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaa ... ccctcctcagTCTAAACATCCAAGATATTCTGGGGAAAACTTGGAGAAGAATAAAGTTCTGTATACACGACTTGAAATGTTGTCCAAGAAGTATGGGTGCACACCTGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTGgtaaatgaaatttacactatcgtaataattttctacagtaatgttattgttagactatgttgtgtatgtgtgtgtggaacatggtttttaaaacggtatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG