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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttttatctcatatggaacatcttatcaggagaaaaaagattcaactctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG

Basic information

species Zea mays
transcript GRMZM2G353147_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g22160.1 (Oryza sativa), 3'ss of exon 7
----gtatcctttttatctcat-atggaacatcttatcaggagaaaaaagattcaactctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG
     |    ||||| | || | ||| |   | ||||     || |     || ||| |  |||  |    |  || ||||  |||||   || |  ||||||||||| || ||||| ||||||||||||||| ||||||| ||||| || |||||||||||||||||||||||||||
gttttttctttttttgtttcgtcatgtagactgttatttatcgagagctatttgaacaccctac--taggttccatgaaaat-ttaaataaaaattgtagGTTCGTGTAATCATTGTGAAACTGGCAGACAGGCTGCATAATATGCGTACACTCACACATATGCCTCAGCACAAGCAG

upper sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G37450.1 (Glycine max), 3'ss of exon 9
gtatcctttttatctcatatggaacatcttatcaggagaaaaaagattcaa-ctctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG
||  ||| ||| ||  | || ||   |  | |      |      || ||  || |||         ||    ||| ||  ||  ||   | | |||||||||| || ||||||||| ||||||| |||||||||||||||||||| ||  ||||||||||||  || || |||
gtgacctctttttcata-atagattcttgtctattcccattcccaatgcattctttgttgaaagcggtttgacaaataacaaatgtctcatttcagGTTCGTGTTATAATTGTCAAATTGGCAGATAGGTTGCATAACATGCGCACGCTATCACATATGCCTCCTCATAAACAG

upper sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G40050.1 (Glycine max), 3'ss of exon 7
gtatcctttttatc-tcatatggaacatcttatcaggagaaaaaa----gattcaa-ctctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG
||  ||| ||| || | ||||         |||    |     |      || ||  || |||         ||    ||  ||| ||  ||   | | |||||||||| || ||||||||| ||||||| |||||||||||||||||||| ||  ||||||||||||  || || |||
gtgacctctttttcataatatattcttctctattcccattcccattcccaatgcattctttgttgaaagcggtttgacaactaataaatgtctcatttcagGTTCGTGTTATAATTGTCAAATTGGCAGATAGGTTGCATAACATGCGCACACTATCACATATGCCTCCACATAAACAG

upper sequence: GRMZM2G353147_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G02260.2 (Arabidopsis thaliana), 3'ss of exon 7
gtatcctttttatctcatatggaacatcttatcaggagaaaaaagattcaactctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG
        |||   || | |   |  |  ||| ||         | |     | | ||  | | |     |  ||    |    ||||| |  |||| || || |||||||||||||| || ||| |||||||||| ||||| ||||||   || |||||||  || ||||||
-------gtttcagtcttttaagattttgtattagc-------tggtgtggttatatatttatcagcatgtctaactgct----tcaatcc--agGTCCGCGTCATTATTGTCAAACTAGCTGACCGGTTGCATAATATGCGAACTCTCTGCCACATGCCTCCCCATAAGCAG

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: 51

GTCTAAGTTGGGGAAACTTCAGTGTAAAAGTGAGGGTAGCACAAAACAAGATATTAAAGCAGAAGACCTAAGGCAGATGTTTCTTGCCATGACAGAAGAGgtatcctttt ... caattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 52

GTCTAAGTTGGGGAAACTTCAGTGTAAAAGTGAGGGTAGCACAAAACAAGATATTAAAGCAGAAGACCTAAGGCAGATGTTTCTTGCCATGACAGAAGAGgtatcctttt ... caattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

GTCTAAGTTGGGGAAACTTCAGTGTAAAAGTGAGGGTAGCACAAAACAAGATATTAAAGCAGAAGACCTAAGGCAGATGTTTCTTGCCATGACAGAAGAGgtatcctttt ... caattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 66

GTCTAAGTTGGGGAAACTTCAGTGTAAAAGTGAGGGTAGCACAAAACAAGATATTAAAGCAGAAGACCTAAGGCAGATGTTTCTTGCCATGACAGAAGAGgtatcctttt ... caattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagattcaactctgtacgttttacttaataaaaaaattaaaatcaattcttagGTTCGTGTGATTATTGTCAAACTGGCAGACAGGTTGCATAACATGCGCACTCTCACACATATGCCTCAGCACAAGCAG
                        acttaat  putative branch site (score: 66)
                                                ttctt  putative PPT
                tacgttttacttaata  TA-rich tract