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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgctctccccatgctgcatttttaaatcttgtgtgtttgattgttgcgttgccacggggctgagcgtttctggcggaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG

Basic information

species Zea mays
transcript GRMZM2G039396_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 2
gttcgtgctctccccatgctgcatttttaaatcttgtgtgtttgattgttgcgttgccacggggctgagcgtttctggcggaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG
||| |||  ||| ||  ||||    ||     ||||    ||   ||||    || | |  | |||||||||||| |||| ||||||||||| || || ||||| |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||||||||||||||||
gtttgtgtgctctccccgctgtgcatt-----cttg---attcacttgtgaaatt-cgattgtgctgagcgtttccggcgaaggtttcagGGGCGTGAGGAGTCGGTGGAGGACTTCGTGCGGCGCAACCTCGGCGCGGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG

upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 2
gttcgtgctctccccatgctgcattttta---aatcttgtgtgtttgattgttgcg----ttgccacggggctgagcgtttctggcggaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG
||  ||  |||  | |   |  |  |  |    || ||  | | || ||  | |       |||    |  || || ||||  |||  ||||  ||||| || ||||| || ||||||||||| || || || |||||||||| |||||| ||||||||||| ||||| || || || ||||
gtgtgtattcttacgaccttttagatcaatatgatttttagggctttatgttggtagaatctgctcatgttcttagagttt--ggcaaaggtgacagGGTCGTGAAGAATCTGTGGAGGAGTTTGTACGGCGTAACCTCGGTGATGAGGTTTTTGAGCGCCTGATTGAACCGTTTTGTTCAG
















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|149005349|gb|EE039900.2|EE039900
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|149071120|gb|EE159520.2|EE159520
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|78079002|gb|DV507414.1|DV507414
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|211265727|gb|FL016769.1|FL016769
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         G-CCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|211265725|gb|FL016767.1|FL016767
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTC-A                         GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAA
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|78087541|gb|DV515934.1|DV515934
EST:     GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         GGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAG
EST: gi|211265728|gb|FL016770.1|FL016770
EST:     GGAAGCTCANGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCA                         G-CCGCGAAGAGTCAGTGGAAGAAGT-CGTGCGCCGCAACCTCGGTGCTGA
genomic: GGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGA-GTTCGTGCGCCGCAACCTCGGTGCTGA

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: 45 (upstream exon), 48 (downstream exon)
Score: 54

GCCATCCAAGCCCGCCGACCTCCCGTTCTTCGATCTCATGAGCATCCCAGGGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

GCCATCCAAGCCCGCCGACCTCCCGTTCTTCGATCTCATGAGCATCCCAGGGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

GCCATCCAAGCCCGCCGACCTCCCGTTCTTCGATCTCATGAGCATCCCAGGGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 85

GCCATCCAAGCCCGCCGACCTCCCGTTCTTCGATCTCATGAGCATCCCAGGGAAGCTCAGGGCCGGTCTAGGCGCGCTTGGCATCCGCCCGCCTCCTCCAgttcgtgctc ... gaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtttgattgttgcgttgccacggggctgagcgtttctggcggaggtttcagGGCCGCGAAGAGTCAGTGGAGGAGTTCGTGCGCCGCAACCTCGGTGCTGAGGTCTTTGAGCGCCTCATTGAGCCTTTCTGCTCAG
    gtttgat  putative branch site (score: 85)
     tttgatt  TA-rich tract