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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaagctcgcacccagcgctctatccatcgcttctgcatttcatccatagcaccaggtagctgagtagtttcggcaaccag

Basic information

species Zea mays
transcript GRMZM2G105631_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105631_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g09930.1 (Oryza sativa), 5'ss of exon 4
GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaacca-agctcgcacccagcgc-tctatccatcgcttctgcatttcatccatagca---ccaggtagctgagtagt--ttcggcaaccag---------------------------------------------
|||||| ||||||| |||||||||||||||||| |||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||| || ||||| ||||| |   | |   ||   |   | ||| | | || |    | | ||  ||  |       | |||     || ||    |||        |                                             
GAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTTCGGCTTCAATGgtaagcttcaaccttcagtaatttcatctgttcttcaccaa-gaactttgtctctgaagattctaggatatagaatatgcattctatgttatgatttttatacataagggctgattgattcggtgaattttcaatcag
















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|211023209|gb|FK976627.1|FK976627
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|37416499|gb|CF645899.1|CF645899
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|33467925|gb|CF244974.1|CF244974
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|37418362|gb|CF646849.1|CF646849
EST:     GTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: GTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|211023212|gb|FK976630.1|FK976630
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCC-TCCTT-GATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|211023210|gb|FK976628.1|FK976628
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCNCCTTCTTTGGATTCAACG                         GCACCGC-GRCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|71330488|gb|DR802010.1|DR802010
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|76018154|gb|DT945324.1|DT945324
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|76020765|gb|DT947935.1|DT947935
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCCCCTTCTTTGGATTCCACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
EST: gi|88757584|gb|DY541725.1|DY541725
EST:     CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACG                         GCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA
genomic: CGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 142

GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 72

GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 37

GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 79

GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaag ... cggcaaccagGCACCGCCGGCGTGTGGCGCATCTCCGCGGTGAACGAGGCTGGGGGGTGGAAGGACCGGACCACGGTGGAGGACATGGATCTGGCCATCCGGGCCAGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTTTGGATTCAACGgtaaaccaagctcgcacccagcgctctatccatcgcttctgcatttcatccatagcaccaggtagctgagtagtttcggcaaccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC