Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgcatccgcttctcctatatcccggtggatctcgccgctgtgtgacttctatgcgaactaccaagtgtggcggcttccttacacgacggcaat...

Basic information

species Zea mays
transcript AC149818.2_FGT001
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC149818.2_FGT001 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g05280.1 (Oryza sativa), 5'ss of exon 1
AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgcatccgcttctcctatatcccggtggatctcgccgctgtgtgacttctatgcgaactaccaagtgtggcggcttccttacacgacggcaat--
||| ||||||| |||||||| |||||||||||||||||||| || ||||||||||||||||||||| | |||||||||||||| ||||| || ||||||||| ||| || || |  | | ||  |  | |  |||||||||  | |   || || ||   |    | |  | | || | |||||||| |       | ||  
AAGATCCTGCTCATCGGGGACTCGGCCGTCGGCAAGAGCAGTCTGCTCGTCAGCTTCGTCTCCGCCTCCCACATCGACGACGAAATCGCTCCCACCATAGgtgcgtacggatgccttccccccgt-cctctctggatctcgttgattcctgcctcctcctcctg-tgctcaatatgtccgcttccttgccttgtcccgatca
















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|211505253|gb|FL326162.1|FL326162
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
EST: gi|71435756|gb|DR816806.1|DR816806
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
EST: gi|211356336|gb|FL310955.1|FL310955
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAAATTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
EST: gi|38229757|gb|CF920070.1|CF920070
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAATTTTGTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
EST: gi|6095558|gb|AW120225.1|AW120225
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC
EST: gi|24462529|gb|BM660060.1|BM660060
EST:     CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAG                         GGGTGGATTTTAAAATCAATTTTGTCAGTGTGGGTGGGAAGAAACTAAAAC
genomic: CAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 28

AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAACTGACAATATGGGACACTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 10

AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAACTGACAATATGGGACACTG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 14

AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAACTGACAATATGGGACACTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 23

AAGGTCCTGCTTATCGGGGATTCGGCCGTCGGCAAGAGCAGCCTCCTCGTCAGCTTCGTCTCCGCCGCTCACATCGACGACGACATCGCGCCAACCATAGgtacgtgcgc ... ctttttgtagGGGTGGATTTTAAAATCAATTTTCTCAGTGTGGGTGGGAAGAAACTAAAACTGACAATATGGGACACTG