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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctagtagttgatttacattatcatataagttgacaaatggattgatctcacctctgtttgtgtctctgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g55260.2 (Oryza sativa), 3'ss of exon 8
---------gtatgtcta---gtagttgatttacattatcatataa-gttgacaaatggattgatctcacctctgt-----ttgtgtctctgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG
          |  | |||     | ||  ||||    ||   |||| | | || ||    ||||         |||     | ||| || ||  | ||||||||| ||||| |||||||| | |||||||||||| || ||||||||||||||| ||||| |||||||||||||| ||||  | || || || |   |||
ggtgcatactttagcctaaagaaacttattttaggacatttgataatgctcactaaacatttgaaaattttgttgtaaccttggtgcctttggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAACTTTTGCCATCAACTACCTCAAAGCTAGAGGTTCCATATGATACTTTAG
















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|60336952|gb|DN203925.1|DN203925
EST:     ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|7216903|gb|AW563025.1|AW563025
EST:     ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|7137663|gb|AW499208.1|AW499208
EST:     ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|76933169|gb|DV173348.1|DV173348
EST:     CGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: CGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|78109694|gb|DV528110.1|DV528110
EST:     GCCGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: GCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|67012372|gb|CO441121.1|CO441121
EST:     ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGG                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
genomic: ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA
EST: gi|9733829|gb|BE512581.1|BE512581
EST:     ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGT                         ATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGCTTGAGGAA
genomic: ATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAA

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: 128

GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 72

GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtctag ... tgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catataagttgacaaatggattgatctcacctctgtttgtgtctctgtccatcagATTCTTGTACCGCTTCCTGAAGGTGAAGCAAGGCAAGCGATGTTTGAGGAACTTCTGCCAGCAACTACCTCAAAGTTAGAAATCCCGTACGACATACTAG
                       atctcac  putative branch site (score: 98)
                                         tctctgtcc  putative PPT