Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaatttctttgcaaagtagcatggattagtggtttgtttcgtatacaggcgtatctttatttcttaactggggctaagttt...

Basic information

species Zea mays
transcript GRMZM2G118014_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g62640.2 (Oryza sativa), 5'ss of exon 6
GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaatttctttgcaaagtagcatggattagtggtttgtttcgtatacaggcgtatctttatttcttaactggggctaagttt-----
 ||| | | |||||| ||||  |||  ||| |||| ||||| || |||||||| ||||||||||||||||| |||||| | |||||||||||||||||||||||| |||| |  |   |  | ||  || | |||||| ||| ||  | ||||  |||| | |    |  ||   |   |   | ||  |||| ||| |      
ACTCCAACACCTCAAATGGCATCAGTACCAGCACCTGCTCCCCCTGATGCTCGCACTCAAGAAATGATCAACGAAAAGATAAAGAAAGCTGAAGAGCTTGgtatgaaaagaaccgctct--actttattactaagtagtatgcatgcg-ggttgttttcttctgtgaggttac--tggctcagttacaagggccaagatatagtt

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G47910.1 (Glycine max), 5'ss of exon 6
GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaatttctttgcaaagtagcatggattagtggtttgtttcgtatacaggcgtatctttatttcttaactggggctaagttt-
   | |  ||| | |     |||| | |  ||   || | | || |||||||| || ||||| ||||| ||||||||||| ||||| ||||| || |||||||  |  ||  || || |   |||| |   | |     ||  ||   |   |   |   |||| |    ||| | ||| | ||   |    ||||  |  
CTGCCAAATCCACCACCTTTGGCACCTCTTCCTGTAGTTGCTCCTGATGCTCGAACACAAGAGATGATAAATGAAAAGCTGAAGAAGGCTGAGGATCTTGgta-agtcagttatatgatctttttcatcttatatatatatatatatatatatatatatatatatatatatatatatatgtttttttttaaactaatatat

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 5'ss of exon 6
------GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatgga--aagcaatgtgtt-gaattt-ctttgcaaagtagcatgg-att-agtggtttgtttcgtatacaggcgtatctttatttcttaactggggctaagttt
      | || | |||  |||   || ||| |   ||      |||| |||||| |||||||||||||||||||||||||||| || |||||||| ||||||||||||| |||  || |    | || | || |  ||||  |  |    ||  ||| | | | | | |   ||      ||| ||  |  | |  || || || |      
CAGGCAGTTCCAGCTCAGCAACCAGCTGCAACTTTAC------CTCCGCCCGATCCTCGTACTCAAGAAATGATCAATGAAAAACTAAAGAAAGCAGAAGAGCTTGgtaaggagcaaacctcttattcgtatctgttttgttatatgtggtgatattgaatcggtagctctttaagttaccgtttcagtggtgcaaaattgtggtt------

upper sequence: GRMZM2G118014_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 5'ss of exon 6
GCTCAACCTCCTCAAGTGGCGGCAGCGCCACC---ACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaa--------tgtgttgaatttctt-tgcaaagtagcatggattagtggtttgtt-tcgtatacaggcgtatctttatttcttaactggggctaagttt
   || ||   || ||      || |  |  |   |  | ||||||| ||| |||| |||||||||||||| ||||| || || ||||| || ||||| ||||||| || ||  ||        ||||||   ||  || |  |  ||    |  |||    | |  || | ||  | ||  | | ||   ||   || |   |         
---CAGCCCGTTCCAGCTCAACCACCATCTTCCGAATTACCTCCACCGGATCCTCGCACTCAAGAAATGATAAATGAGAAACTGAAGAAGGCAGAAGATCTTGgtaagggaaataaccctaatttgtgtttggttatttgtctatggtcatcttaatttagagctcattgtagtggaaagttgaaactgc-ttaaatatccacg---------

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|71445995|gb|DR827045.1|DR827045
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
EST: gi|211400936|gb|FL417155.1|FL417155
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
EST: gi|149079348|gb|EE168324.2|EE168324
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGGAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
EST: gi|211517989|gb|FL372294.1|FL372294
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
EST: gi|211311591|gb|FL416726.1|FL416726
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
EST: gi|76020071|gb|DT947241.1|DT947241
EST:     TCGTACTCCAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAAAAAGCTTT
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTT
EST: gi|211019421|gb|FL374991.1|FL374991
EST:     TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTG                         GGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG
genomic: TCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAG

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: 166

GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 47

GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 69

GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaag ... attttggtagGGGAACAAGGCATGGTTGATGAAGCTCAGAAAGCTTTGGAAGAGGCAGAAGCTCTGAAAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCAACCTCCTCAAGTGGCGGCAGCGCCACCACCAGCTCCACCCGATGCTCGTACTCAAGAAATGATCAATGAAAAGCTTAAGAAAGCTGAAGAGCTTGgtatggaaagcaatgtgttgaatttctttgcaaagtagcatggattagtggtttgtttcgtatacaggcgtatctttatttcttaactggggctaagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT