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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagattatctgtaaccatcacctacatatttatgagaactggggacgaccttttgtattcactctcatttatctttattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 22
gtacagattatctgtaaccat-cacctacatatttatgagaactggggacgaccttttgtattcactctcatttatctttattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT
||   |||  |    | || |  |   |||| |  |       |      | |||  | | ||    ||||||  | || ||| | ||||| | |||||| || ||||||||||||||| |||||| ||||||||||||| ||||||||||  |||||||||| ||||||||||||||||||||  | |
gttaggatggtgaccacccttatattcacatctggacacttgatctttttggcctgatctttttggcctcattc-ttttcatt-tgcagGGTTGCATTCCTGGTGGTGCTGTTAAACCTGTTGATGATGTTCCAGAGGCCCATTTTGATGTTACTGAGCATTATTGGTTTCCTATGCTAGCTGGCCTAT
















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: 328

TGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAGTTTGAAGGCTATTGCTCTCCTGCGTATATGTGAAGATCGTTTGGCAGAGgtacagatta ... tattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

TGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAGTTTGAAGGCTATTGCTCTCCTGCGTATATGTGAAGATCGTTTGGCAGAGgtacagatta ... tattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 157

TGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAGTTTGAAGGCTATTGCTCTCCTGCGTATATGTGAAGATCGTTTGGCAGAGgtacagatta ... tattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 315

TGTCAACTGTCTTATTGGTTTTGCAAATAACAAGTGCACTCCTCGGATTAGTTTGAAGGCTATTGCTCTCCTGCGTATATGTGAAGATCGTTTGGCAGAGgtacagatta ... tattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgagaactggggacgaccttttgtattcactctcatttatctttattgtacagGGATTCATTCCAGGCGGTGCTGTTAAACCTATTGATGTTGTTCCAGAGGCCAATTTTGATGTGTCTGAGCATTACTGGTTTCCTATGCTAGCTGGTTTGT
                               ctctcatttatcttt  CT-rich tract
                                    atttatctttattgta  TA-rich tract