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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaactgcatccaatccaatacaagacactagcaccctgttcttgacgggtttttgtggaaattgtctttggtctaacatactatggcgcaaaacttctagtagaaattgctgcgtaccttgtatattgcaccagttttgttggttcctccgctaaacctgtctctgctccatgtag

Basic information

species Zea mays
transcript GRMZM2G011078_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011078_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 5'ss of exon 4
GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaactgcatccaatccaatacaagacactagcaccctgttcttgacgggtttttgtggaaattgtctttggtctaacatactatggcgcaaaacttctagta--gaaattgctgcgtaccttgtatattgcaccagttttgttggttcctccgctaaacctgtctctgctccatgtag
|| ||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| |||||||||     ||| |    || ||  |||      ||||  | ||| |||    |  |||      |||| | |            ||||||  |  ||| || | ||    | || | |  | |   ||| ||     |   ||  || | || |  |  || |                    
GATATGAAAACAAGGGAGAAGGAACTTCTTGCAAAGGAAGCCGAGCTAAACAGGCGAGAGAAGgtaac---ctgaacatgatgcagaacag--tgttagctgcatgtacttccttgaatttc-----aattctttcca---------actatgttggcaaagttgttgtgccaagatggatttg-attatgtgtaacatgctgatt--gtcgcttacgtctgtatag-------------------
















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|76927248|gb|DV171197.1|DV171197
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|76280658|gb|DV020226.1|DV020226
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|71440939|gb|DR821989.1|DR821989
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGGCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGGACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|76282431|gb|DV021999.1|DV021999
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|78092064|gb|DV520438.1|DV520438
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|89760517|gb|DY688893.1|DY688893
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|78080153|gb|DV508565.1|DV508565
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG
EST: gi|76928466|gb|DV171634.1|DV171634
EST:     GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG                         GAAATAAAAAGGCGAGAAGATGCTGCGGCACGAG
genomic: GGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG

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: 44

GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 430

GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 490

GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 92

GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaact ... ctccatgtagGAAATAAAAAGGCGAGAGGATGCTGCGGCACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAGgtagtaaactgcatccaatccaatacaagacactagcaccctgttcttgacgggtttttgtggaaattgtctttggtctaacatactatggcgcaaaacttctagtagaaattgctgcgtaccttgtatattgcaccagttttgttggttcctccgctaaacctgtctctgctccatgtag

- - - - - - - GGAGAA
- - - - - - - - - AAGGAG
- - - - - - - - - - GGAGCT
- - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGCTGA