Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctctcccaccaattcaggattcagttgttttgccactttcgtgccttgtgaaatagctctaggccctgctattcttgcag

Basic information

species Zea mays
transcript GRMZM2G060870_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 5'ss of exon 6
ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctctcccaccaattcaggattcagttgttttgccact-----ttcgtgccttgtgaaatagctctaggccctgctattcttgcag
||| |||||||||||||||||||| ||||| || || || ||||| |||||||| ||||||||||| |  |||||||||||||| ||||| || |||||||||||| ||||| ||    || | |  | |||  ||| | |  |     |  |   ||  ||  ||  ||      | | ||||||||||||
ATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctctcacatt--ttgaaggcttagtcctttagtctgtaattgtctgattctaatgtgatgtcttcca-tcatactattcttgcag

upper sequence: GRMZM2G060870_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G00690.2 (Glycine max), 5'ss of exon 5
ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctctcccaccaa--------ttcaggattcag-----ttgttttgccactttcgtgccttgtgaaatagctctaggccctgctattcttgcag-
 || ||| | || ||  | || ||||| ||||||||||| ||||| ||||||||||| || ||||| |||||| | ||  |||| | |||| ||||| ||||| |  ||  |  | |          || | || | |      | ||    | || ||  |      |||| | |     | |  ||  ||   ||||  
GTTTATGAACGTGATAGGAGGCACTGGCGATATCAATGCTGATATCGAGAAATTTTGTACAACCTTTTCTCCTCTCCTTCAAGAGATTCACAAGTTTTTGgtaagaactaacatatcttggattatttttatgacttaaaatgatagtaaaacgacatttat-ttgaatgaactggaagatgacattgaaatgtatgcatc
















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|32934286|gb|CF039098.1|CF039098
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAA-TCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32932161|gb|CF036973.1|CF036973
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32866744|gb|CF006426.1|CF006426
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32934643|gb|CF039455.1|CF039455
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32930749|gb|CF035561.1|CF035561
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|45567822|gb|CK985763.1|CK985763
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|60346084|gb|DN213057.1|DN213057
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     ATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAAATCACGAGTTTCTG                         GCGAGCGTTGGCCTTGATGATATGAAGGC
genomic: ATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAA-TCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGC
EST: gi|211296158|gb|FL473352.1|FL473352
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|17932440|gb|BM269400.1|BM269400
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|6056907|gb|AW091312.1|AW091312
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|211377984|gb|FK983375.1|FK983375
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAA-GAAAATCACGAGTTTCTG                         GCGAGCGGTGGTCTTGATGATATGAAGGCTTCGTA
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTA
EST: gi|60401114|gb|DN233921.1|DN233921
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|5686769|gb|AI939862.1|AI939862
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|84351358|gb|DW245763.1|DW245763
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCCCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|87157246|gb|DY402035.1|DY402035
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAG
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAG
EST: gi|60401080|gb|DN233887.1|DN233887
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32932571|gb|CF037383.1|CF037383
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32932862|gb|CF037674.1|CF037674
EST:     CTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: CTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|71770686|gb|DR968623.1|DR968623
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32840612|gb|CD980293.1|CD980293
EST:     ATTTTGCAC-AGCCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: ATTTTGCACGA-CCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32935206|gb|CF040018.1|CF040018
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCCCGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|60399775|gb|DN232585.1|DN232585
EST:     AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|211375011|gb|FL430792.1|FL430792
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|211296159|gb|FL473353.1|FL473353
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32932100|gb|CF036912.1|CF036912
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|211365280|gb|FL463922.1|FL463922
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
EST: gi|32867861|gb|CF007543.1|CF007543
EST:     AATTTTGCACAACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTG                         GCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT
genomic: AATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGT

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: 104

ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGTGGTGATTACAACAAAATAAGCGTGTCTTATCAAACTCAAGTGTTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGTGGTGATTACAACAAAATAAGCGTGTCTTATCAAACTCAAGTGTTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGTGGTGATTACAACAAAATAAGCGTGTCTTATCAAACTCAAGTGTTGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctc ... attcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGTGGTGATTACAACAAAATAAGCGTGTCTTATCAAACTCAAGTGTTGCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATGGAGGTCATTAGTGGAACTGGTGATATCAATGCAGATATTGAGAAATTTTGCACGACCTTCTCTCCTTTTCTCAAAGAAAATCACGAGTTTCTGgtatggtctctcccaccaattcaggattcagttgttttgccactttcgtgccttgtgaaatagctctaggccctgctattcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA