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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgacctcccctctagccacattctccatttctctttatttgtaggttatctagactgaaaaactgaacatatttgtatctgccaatgctgatggaactgtgggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 9
gcatgacctcccctctagccacattctccatttctctttatttgtaggttatctagactgaaaaactgaacatatt-tgtatctgccaatgctgatggaactgtgggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC--
                   ||   || ||| | || || |||| |   |||||      | ||     || ||||| |  || |||  ||  ||    |  |||   |||| ||||||||||||||| ||||| ||||||||||| ||| ||||||||||||  || |||||||   ||   |||  | |||||||||| ||||||||    |    
------------------gcatgatccccaatcctgttcatttat---ttatc------ggaagttctaaaatattgtagatttgctgatcttggc--acttgt---atgttcagGGTGAGCCCTTCTAAGACACCGGTGAAGCCACGTTTAAATCGAGTGGCGTCGAACTGACC--GCTTGAGCCAAGCTGGATTGTTTACGGGAAGATCGCTTAA
















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|5058613|gb|AI737089.1|AI737089
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|4609957|gb|AI600796.1|AI600796
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|37392334|gb|CF633416.1|CF633416
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATATTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|32836018|gb|CD975696.1|CD975696
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|78106612|gb|DV525030.1|DV525030
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|61236519|gb|DN586269.1|DN586269
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|12046008|gb|BF728043.1|BF728043
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|32933652|gb|CF038464.1|CF038464
EST:     GCAGCGGGATGATTTTGGGAACCACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGCGTAAATCGAGTGGGATC
genomic: GCAGCGGGATGATTTTGGGAA-CACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|28983351|gb|BQ538610.2|BQ538610
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAAC-CTGCCTGTCAG                         GGTGAGCCCTTC-AAGACTCCGGTGA-GCCC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCC
EST: gi|4804027|gb|AI665893.1|AI665893
EST:     ATCATGGCTTTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|211050111|gb|FL461721.1|FL461721
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|109179585|gb|EC380089.1|EC380089
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
EST: gi|6827432|gb|AW331075.1|AW331075
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAG                         GGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATC

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: 45 (upstream exon), 49 (downstream exon)
Score: 86

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 113

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACACTGCCTGTCAGgcatgacctc ... ggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaactgaacatatttgtatctgccaatgctgatggaactgtgggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC
                             tgctgat  putative branch site (score: 113)
            atatttgtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgacctcccctctagccacattctccatttctctttatttgtaggttatctagactgaaaaactgaacatatttgtatctgccaatgctgatggaactgtgggatgtccagGGTGAGCCCTTCCAAGACTCCGGTGAAGCCCCGTGTAAATCGAGTGGGATCTAACTGACTCTGCGCAAGCTGAACTGGATTGTTCACGGGAAGGCGTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA