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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgatgttccctatcatccatggtttatcttgctgtgctgtgctgattcctatccatctcccattaacttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG

Basic information

species Zea mays
transcript GRMZM2G178460_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178460_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 3'ss of exon 3
gtgcttgatgttccctatcatc----------------catggtttatcttgctgtgctgtgctgattcctatccatctcc--cattaacttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG
||||||||| ||||| |||||                 |||||||||| ||  | || ||  |   |||  |   |  | |   || ||||  |  |||| || |||||| ||||||||||||| |||||||| || || |||||||||||||||
gtgcttgatattccccatcatgcagattgtggctcatgcatggtttattttattctgttggtcctgttctcacttagtttctttataaactacttaagGTTATCCGCATAGTTCCTTACAGTGCGGTGCAACTGTTTTCTTATGAAGTTTACAAG
















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|71423587|gb|DR806089.1|DR806089
EST:     TTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAG                         GTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTT
genomic: TTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAGgtgcttgatg ... acttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTT




















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: 114

GCTATGGCAGACATTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAGgtgcttgatg ... acttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GCTATGGCAGACATTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAGgtgcttgatg ... acttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG


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

GCTATGGCAGACATTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAGgtgcttgatg ... acttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GCTATGGCAGACATTGGAAAGAAGGATGGGCTTAAGGGTTACTGGAAAGGAAACCTTCCACAGgtgcttgatg ... acttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttatcttgctgtgctgtgctgattcctatccatctcccattaacttgtccagGTCATTCGCATAATTCCTTACAGTGCAGTGCAACTCTTCTCGTATGAAGTTTACAAG
                                        cattaac  putative branch site (score: 100)
                                              cttgtcc  CT-rich tract
                                         attaactt  TA-rich tract