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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgttcacgattaaaccaatccatagtgaaattcttcttatgtattccattttttctgtaccatggaaatgctttagtttgtcacttatgttta...

Basic information

species Zea mays
transcript GRMZM2G108087_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108087_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g47440.1 (Oryza sativa), 5'ss of exon 3
ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaac-cctgttcacgattaaaccaatccatagtgaaattcttcttatgtattccattttttctgtaccatggaaatgctttagtttgtcacttatgttta----
|||||||  | || ||||||||||   | |||||||| | |||||||||||| ||||||| ||||||||||||||||||||| ||||   | ||| ||||||||  | ||| |||  || |  | || |||  | ||| | ||||  ||||||    |||   |||  |||     |||  |  | || || |  | ||||    
ATTTTGCCACGACGATGGAGGAGTATGGAAAACTTCAAAATCTTGCGATTCAAAGGGAGATGGCATATAAGCCAGTTGTTCCCCAGACATCTCAGCCAAAgtaatgcttgtacacttttcattcgattcatc-tcaaacttttctc-tgtattg---tttgattgtttcattttcctgccatgatatgccattggtttttaatag
















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|89251975|gb|DY623761.1|DY623761
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74235067|gb|DT642981.1|DT642981
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|211183486|gb|FL441241.1|FL441241
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|76286077|gb|DV025645.1|DV025645
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78093274|gb|DV521648.1|DV521648
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAA
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAA
EST: gi|74234506|gb|DT642420.1|DT642420
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74239521|gb|DT647435.1|DT647435
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|60336907|gb|DN203880.1|DN203880
EST:     CAGAGGGAGACGGCATATAAGCCAATTGTTCCACATAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78117098|gb|DV535485.1|DV535485
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|211183485|gb|FL441240.1|FL441240
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|74234352|gb|DT642266.1|DT642266
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|78074309|gb|DV502743.1|DV502743
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|89756275|gb|DY686358.1|DY686358
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
EST: gi|71768040|gb|DR965977.1|DR965977
EST:     CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAA                         CTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG
genomic: CAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCG

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: 48 (upstream exon), 49 (downstream exon)
Score: 51

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

ATTTTGCTGCCACAATGGAGGAGTTCAGGAAACTTCAGAGTCTTGCGATTCAGAGGGAGACGGCATATAAGCCAGTTGTTCCACAGAATACGCAGTCAAAgtaaccctgt ... tgtgatgcagCTATTCTACAGATGAGCGAAGTTCCGAATCTGGTAATATGCCTGAGCAGCGTGCATTACTCGCTGAATCAATGAG