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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcttgacccaggtccattattttgtagtactgttatggattttatgttcatatagtaggcgtagaaaccaataatcaatttatgctataaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 10
gatcttgacccaggtccattattttg-tagtactgttatggattttatgttcatatagtaggcgtagaaaccaataatcaatttatgctataaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC
 |      ||   ||| | || |||| ||    ||||||||   || || || |  |    |     ||||   |      |||| |  |||| |||  |||||||||||||||| |||||||||||||||||||||||| |||| |||||||| |||||||||||  | || |  | || |||||||| ||| |||||||
taatgcatcctctgtctactaatttggtatggttgttatggcaatt-tgatcctgaaactagtaggcaaacatcttgattgtttacgtcataattctttagGTGGATGGTGATACGAGTACCAATGACTGTGTTATTGCTCTGGCTAGTGGGTTATCTGGTTTATCCAGTATCCTTACTCATGATAGCACTGAAGCTCAAC

upper sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G19450.2 (Glycine max), 3'ss of exon 11
gatcttgacccaggtccattattttgtagtactgttatggattttatgttcatatagtaggcgtagaaaccaataatcaatttatgctataaat--ctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC
      ||       ||| | |  ||| || |  |   | |  || ||  |  |   |  |  | | ||   ||    |  || |||  ||  |  ||  |||| ||||| ||||||||||| |||||   |||||||||  |||| ||||||||||||||  |   | | ||      ||| || ||   |||||||   |
-caaaagattattagccaatttaatgtggtgccatc-cgaagcttttgcccccaatttttggattgtaattgattcctatgttttgcattattttgctacagGTAGATGGAGATACTAGTACTAATGATACTGTTATTGCCTTGGCTAGTGGGTTGTCTGGGCTTGGTTGCATATCTTCTCTAGACAGTGATGAGGCTATTC

upper sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 10
gatcttgacccaggtccattatttt--gtagtactgtt-atggattttatgttcatatagtaggcgtagaaaccaataatcaatttatgc-tataaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC
    || |    | ||  || |     || || |  |  |  ||||||     ||  |  | |   | | ||   ||    |  || ||| |||    ||  |||| ||||| ||||||||||| |||||   |||||||||| |||| ||||||||||||||  ||    | ||      ||| || ||   |||||||   |
--atttaatgtggttctcttgtgcaaggtggtgccatccaaagattttgcccccaatttttgg--attgtaattgattcctatgttttgcatattttgctacagGTAGATGGAGATACTAGTACTAATGATACTGTTATTGCTTTGGCTAGTGGGTTGTCTGGGCTAGGCTGCATATCTTCTCTAGACAGTGATGAGGCTATTC

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|78092275|gb|DV520649.1|DV520649
EST:     GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA                         GTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG
genomic: GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA                         GTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG
genomic: GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA                         GTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG
genomic: GGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGG

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: 199

GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 117

GTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACAgtgagtctct ... aaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttcatatagtaggcgtagaaaccaataatcaatttatgctataaatctgaagGTGGATGGTGATACTAGTACCAATGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAAC
                          aataatcaatttatgc  TA-rich tract