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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgaccaagatattttttggttggatttatgaactttttaggtatctctaacatggtcacaatcatccttgctgcag

Basic information

species Zea mays
transcript GRMZM2G475867_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G475867_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 5'ss of exon 21
GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgaccaagatat-tttttggttg---gatttatgaactttttagg--tatctctaacatggtcacaatcatccttgctgcag
|||||||||||||||||||  |||||||||||| ||||||||||||||| ||| ||  |||||||||   | ||  | || || ||| |||   | |||||||||||| || |  | || || || || | |||| || | |||| |   
GTTTTGGTGGATCTCTTTCGACATGATTTGCGACTGTGGAAAGCATATAACATCACCTTACAGgtttacaatcataaaatattcttgtttgtacggtttatgaactttctaagaatgtccctgacttgcttacaaacaac-ttgcag---
















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|5871549|gb|AW018020.1|AW018020
EST:     CATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: CATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|71760706|gb|DR958643.1|DR958643
EST:     TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|78024464|gb|DV492851.1|DV492851
EST:     TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|12969124|gb|BG266069.1|BG266069
EST:     TTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: TTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|5018261|gb|AI714454.1|AI714454
EST:     TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|9952965|gb|BE639548.1|BE639548
EST:     TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
genomic: TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAA
EST: gi|9952966|gb|BE639549.1|BE639549
EST:     TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAG                         TCACATGATGTATTCAGGGAA
genomic: TCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAA

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: 47 (upstream exon), 48 (downstream exon)
Score: 18

GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAACAGCTTTCGTCTGTCTCTGATCTTACATTGCAGAATGGACCATTGTCAT


Block sizes: 40 (upstream exon), 27 (downstream exon)
Score: 9

GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAACAGCTTTCGTCTGTCTCTGATCTTACATTGCAGAATGGACCATTGTCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 9

GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAACAGCTTTCGTCTGTCTCTGATCTTACATTGCAGAATGGACCATTGTCAT


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 7

GTTTTGGTGGATCTCTTTCAGCATGATTTGCGATTGTGGAAAGCATATAGCATTACTCTACAGgtttgtgacc ... cttgctgcagTCACATGATGTATTCAGGGAATATCTTGACCTTCTTAATATCTTGGAGGAACAGCTTTCGTCTGTCTCTGATCTTACATTGCAGAATGGACCATTGTCAT