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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgcttgctgctaggtcttagagagctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA

Basic information

species Zea mays
transcript GRMZM2G108457_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108457_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g36440.1 (Oryza sativa), 3'ss of exon 12
gtaagtt--aattttactgtgtctgtcactgaacagggatagcttaatgtttcagcaagatagaattagtcacgtgctt-gctgctaggtcttagagag-ctgaactctcgacgaacaatgctacgagaatggttcgtgactcacaatttctttttactgctttacccttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATC-AGACAGTTGAAAATGGA
|||||||   |||  |||        |    ||       || || | |  |  | |   |    |  || | |  ||| |   ||| |   |||||||  |   ||   || ||||||   || |   ||  |    ||   |  |  | | ||| |||||||   | |  ||||||||| || |||| |||||| |  |||||||| |||||||||||||| ||||||||||||||||| ||||| ||| | ||||   | | || |     ||  
gtaagttcagattccactaacatccccctaaaatgaactgagtttgaaggattgggagctttatttatgttagggtcttagggactaagaagtagagagatttgtctgctgatgaacaaca-taagctgatattggcagaaaaatgacgtttgtttgctgctttgatcctcatccagGACTGGAACAAAGATCTCCTGTACTAGATGCGGGTCTTCTTGGGCTCCTCAGATGGTTGAGAACGCTTGCTTAGGATGATACGGACAAAGATTTGGTTGA-
















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|149086468|gb|EE176013.2|EE176013
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|211081518|gb|FL472798.1|FL472798
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|60336973|gb|DN203946.1|DN203946
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|71431774|gb|DR812824.1|DR812824
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|86471657|gb|DY238027.1|DY238027
EST:     TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
genomic: TGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA
EST: gi|166615281|gb|EG315468.1|EG315468
EST:     GGATCATGTGCGCTCACCGAGTCGCTGCAGATATTG                         GACTAGAGCAAAAATCTCCGGCTCTAGATGTTGGTCTTCTTGGGCTACTCA
genomic: GGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCA

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), 41 (downstream exon)
Score: 29

GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 29

GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 26

GGCCTTTACTGTGTTGGTGACAGCTGTTTTCCCGGACAAGGTGTAATAGCTGTAGCATTCTCAGGGATCATGTGCGCTCACCGAGTCGCTGCAGATATTGgtaagttaat ... cttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgagaatggttcgtgactcacaatttctttttactgctttacccttattccagGACTAGAGCAAAAATCTCCGGCTCTAGATGCTGGTCTTCTTGGGCTACTCAGATGGTTGAGAACACTTGCATAGAACGATATCAGACAGTTGAAAATGGA
                gactcac  putative branch site (score: 26)
                         tttctttttactgctt  putative PPT
                     acaatttcttttta  TA-rich tract