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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcag

Basic information

species Zea mays
transcript GRMZM2G113476_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113476_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g38850.1 (Oryza sativa), 5'ss of exon 5
GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaa-tagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcag--tagtaaa-gttgtgcttcatctactgacattca--ttcagagatgaacatcatatttaac-ctgtttggtatttttatatatgcag
|| |||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||||| ||||||| ||||| ||||||     || ||   ||  |    |    ||   | ||   || |  || |||  | |||| ||   | ||||| ||| || | |||||  |  ||  ||  ||||||||||| ||| |||| |||  |  | || ||| ||| ||| |||||
GTCCGTGGTTTTCTTCTCAACTTTGGTGTGTACTATGCTACTAGAGCAGCACTGGGTCTTACATTCCAATGGAGgtaaaatagtcaccggaaaattcttta----tgcttaatcagtaccaattagctttatttttagatattagatatcctctgcctatcaaattggtaaaagttctgttacatctcattgcagacagattcagagatgatcattatatctaatgccatatgatatctttctatctgcag

upper sequence: GRMZM2G113476_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT3G11945.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtcac-tggaaatttctttggaactgtttctgcataa-agggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcag
|| || ||||||||||| |||||||| |||||| ||||||| || ||||| || || ||| |||| || |||||||   ||||||  || | |   |||   ||     ||   |||| ||| |  | || || || |    ||  ||     ||   ||   ||     |                                                                           
GTACGAGGTTTCCTTCTTAACTTTGGTGTGTACCATGCTACAAGAGCTGCTCTTGGACTTCCATTTCAGTGGAGgttggtagtcaaatgcacaaaacttaataaacaggtcgtaataataggatggactttgc-atacttgtatggatagagttttaatatatgtgagggaccaa-----------------------------------------------------------------------
















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|13558184|gb|BG549540.1|BG549540
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCAT
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCAT
EST: gi|71445925|gb|DR826975.1|DR826975
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGCTT
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTT
EST: gi|148973603|gb|EE024711.2|EE024711
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGC
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGC

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: 39 (upstream exon), 49 (downstream exon)
Score: 35

GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 26

GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

GTTCGTGGTTTCCTTCTCAACTTTGGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA