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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcctaccctgccacacgtgtagagcctgattgaacgcgcctgcatgttcttgttctgtcttgtgattttgtctcgaccaatcaaagccaaactaacttggtgatctgcttttctgctgcggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG

Basic information

species Zea mays
transcript GRMZM2G383408_T01
intron # 4
splice site 3'
intron type U2

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|16745979|gb|BM032409.1|BM032409
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|149084763|gb|EE174260.2|EE174260
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|18385015|gb|BM418214.1|BM418214
EST:     TGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGAT-AGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|22489287|gb|BU049210.1|BU049210
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|89106281|gb|DY576498.1|DY576498
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|148947740|gb|EC893223.2|EC893223
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|18384701|gb|BM417900.1|BM417900
EST:     GGATGG-TCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: GGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|18053160|gb|BM318818.1|BM318818
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATA
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATA
EST: gi|91870307|gb|EB400808.1|EB400808
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|8367862|gb|BE050807.1|BE050807
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
EST: gi|149074060|gb|EE162401.2|EE162401
EST:     TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATG                         TCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC
genomic: TGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCC

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: 44 (upstream exon), 49 (downstream exon)
Score: 93

GAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 125

GAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

GAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

GAATACGGGATATTGCTGGAAGTGATCCAGGTCATGATTGATCTCAACCTTGTCATAGGCAAGGCATATATAACCTCGGATGGTGGATGGTTCATGGATGgtgagctcct ... cggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaccaatcaaagccaaactaacttggtgatctgcttttctgctgcggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG
                aactaac  putative branch site (score: 222)
     aatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcctaccctgccacacgtgtagagcctgattgaacgcgcctgcatgttcttgttctgtcttgtgattttgtctcgaccaatcaaagccaaactaacttggtgatctgcttttctgctgcggtgttcagTCTTCAATGTGACCGATAAGGAAGGGAAGAAGATCAAAGATGAGGCAACCCTCACACAGATCGAAGACTACATCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA