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

...gctgggcctagttggcccgacttgggcccaacgcctccgtagcccatcacggctatttaggcctgtgacagtttctcacgcaatgtaacttctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC

Basic information

species Zea mays
transcript GRMZM2G116151_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 4
gctgggcc-tagttggcccgacttgggcccaacgcctccgtagcccatcacggctatttaggcc-tgtgacagtttctcacgcaatgtaacttctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC
  ||   | || ||   |       |  | ||       | |     ||     ||  |||      |||   | ||| | ||||   ||||| ||| ||||||||||||||||||||| |||||||| |||||||||||||||||||| || |||||
-ttgattcataattaatcatgaacagagcaaaattaaatggattggttcttcattacctagaaaacatgaagttctctgatgcaaaccaacttatat-gcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 4
--------------gctgggcctagttggccc--gacttgggcccaacgcctccgtagcccatcacggctatttaggcctgtgacagtttctc-acgcaatgtaacttcta-----ttgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC
              ||||   || |||||      | ||  |     |  ||  | ||    |   | || |||   | |     ||  | ||   |  ||  ||   ||      |||||| ||||||||||| | || |||||| | ||||||||||||||||||||||||||| |
gtatgctatcatttgctg--tcttgttggttatgaatttatggtggtcaactgtggagtttctttagtctgtttctccttaatttagaatgtctgtgtgatagaaaacctgaatggttgcagGTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACAC
















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|30306558|gb|CD001231.1|CD001231
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACAT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACAT
EST: gi|101387539|gb|EB815784.1|EB815784
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     CGTACCAAGAGTACACTACAAAGGGAAGCTGGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCCTATGGGATGTTTGGGAATAATAACT
genomic: CGTACCAAGAGTACACTACAAAGGGAAGCTGGG-AGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCC-TATGGGATGTTTGG-AATAATAACT
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
EST: gi|211200247|gb|FK978071.1|FK978071
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCTAT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTAT
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATG                         ATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT
genomic: GCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCT

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), 46 (downstream exon)
Score: 90

CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 67

CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 36

CACTCTTAGCGGAATTCATGGCGTACCAAGAGTACACTACAAAGGGAAGCTGGGAGAGTATTATATCATGgtattgagca ... tctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacggctatttaggcctgtgacagtttctcacgcaatgtaacttctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC
                                           cttctatt  CT-rich tract
        tattta  TA-rich tract