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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaaggaagctcgtaatctgttttagatatttttatattataaaatatgggagttttaaatacttatattttttgggttgaaaatttgctag

Basic information

species Zea mays
transcript GRMZM2G176698_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176698_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g10420.2 (Oryza sativa), 5'ss of exon 11
ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaaggaagctcgtaatctgttttagatatttttatattataaaatatgggagttttaaatacttatattttttgggttgaaaatttgctag
 ||||| ||||||||||||||||| || || || || |||||||||||||| || || || || |||||||||||||| || || ||||| || ||||||||| || || |||| ||||      ||| |  || |  ||   |||||| | | | || |||  | || | ||      || |  |   || |||
GCATATAATTCATATTGATTTTGGCTTTATGCTTTCCAACTCTCCTGGAGGGGTTAATTTTGAAAGTGCACCATTTAAACTGACAAGGGAGCTTCTTGAAgtaagatggtagcttgtaac-----ttaaactttatggtagattaaaatgttgaa-ttataataaattttgtt------gtggggaccatggtag
















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|32930699|gb|CF035511.1|CF035511
EST:     GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAA                         GTGATGGATTCTGATGCAGAGGGAA
genomic: GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAA
EST: gi|32931844|gb|CF036656.1|CF036656
EST:     GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAA                         GTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTT
genomic: GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTT
EST: gi|211143140|gb|FL283868.1|FL283868
EST:     GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAA                         GTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTT
genomic: GTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTT

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), 48 (downstream exon)
Score: 168

ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTTAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 130

ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 180

ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTTAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 133

ACATATTATTCATATTGATTTTGGTTTCATACTGTCGAACTCTCCTGGAGGTGTAAACTTCGAGAGTGCACCATTTAAGCTAACGAGGGAACTCCTTGAAgtatgaagga ... aatttgctagGTGATGGATTCTGATGCAGAGGGAACTCCCAGTGAGTTCTTTGATTACTTTAAG