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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgacatgtttttgtttggccctttacttttttatggcagattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 26
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 43
gtttgac-atgtttttgtttggccctttacttttt-tatggca-gattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC
|||||    |||  |  |||  || ||| || ||| | |||    || || ||||| |       | |||| | ||  ||||| || |||||||||||||||||||||||||||||||||||||| || || |||||||| || ||| |||| ||||||||||||||||||||||||||||
gtttgtttgtgtactcttttctccttttgctctttgtttggttcaatgttatttatgta------taggctgtattt-cagACTTTCCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACTCTAGATAACCTTATCACAGAGCTACTACTTTGGCTCTTAGATGAAAGGGTTCCTC

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 26
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 15
------------gtttgacatgtttttgtttggcc-ctttacttttt-tatggcagattttgtttatctgaaatcttgggctattttga--------cagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC
             |   | || |   |  ||| |  || |||| |   |   | | || |  | | ||  |||   |   ||| || ||        |||||||||||||  |||   |||||||||||||| ||||||  ||| |||||||  ||||| || ||| |  | |||||||| || ||||||||||||||||
ataaaaataaaaataaaaaatctggattcttgacaactgtactgtgcatgaaggaaatgtattatgtcacaaaaacttaactacttggagttttttgcagACATTTCAGAATAAAAAACTTGCTCATGCTGTCAAGGAGTCTACTCTTGACAGTCTTATCACTGAGCTTTTGCTTTGGCTTTTGGATGAAAGGGTTCCTC
















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|18649605|gb|BM498424.1|BM498424
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACG
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACG
EST: gi|20301651|gb|BQ164594.1|BQ164594
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|18450492|gb|BM428770.1|BM428770
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGCGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|19822548|gb|BQ048572.1|BQ048572
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACG
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACG
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|18450764|gb|BM429042.1|BM429042
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|18648832|gb|BM497651.1|BM497651
EST:     CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGAC
EST: gi|18648721|gb|BM497540.1|BM497540
EST:     CTGGGGCTTCTTCAAGGNCTTGCAAATATGNCTTAAACACACTCATGCAG                         ACATTTCAGATCAAACG
genomic: CTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACG

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: 269

GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 44

GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAGgtttgacatg ... attttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacttttttatggcagattttgtttatctgaaatcttgggctattttgacagACATTTCAGATCAAACGTCTTGCTCATGCTGTGAAGGAGGGTACCCTTGACAACCTTATTACGGAGTTACTTCTTTGGCTCTTAGATGAAAGGGTTCCTC
                                           ctatttt  CT-rich tract
                   attttgtttat  TA-rich tract