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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA

Basic information

species Zea mays
transcript GRMZM2G171406_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43594.1 (Oryza sativa), 3'ss of exon 3
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                         |  | |   | ||| |     | || || |    ||| |   |||| |||  ||   |  ||  ||||| | | ||           ||||||||  |  |||   ||||||||||||||||||| || |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |
-------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctga-aacctggcaagaagatttgatg---------caaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAA

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g43594.2 (Oryza sativa), 3'ss of exon 4
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA------------------
                         |  | |   | ||| |     | || || |    ||| |   |||| |||  ||   |  ||  ||||| | | ||           ||||||||  |  |||   ||||||||||||||||||| || |||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |                  
-------------------------gcgcccaaaaaaatgttacaatatttcttgacagaaacctc-ccagattttctga-aacctggcaagaagatttgatg---------caaatttgttctttttccattcagGTCAAAACAACATCACCAAGGAAGTATTTCGTCCGGCCGAACGCGAACATCGTCCAGCCATGGGATTCTTGCACAATAACAAGTAAATACATGTTTCCAA

upper sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 3
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                                                  |  |   |     |    || |    || ||        ||     | |||  |||| || | ||||||        | |||||||||||| || ||||| |||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||||||||| |
--------------------------------------------------gtccatggccttccatttcatgaccaatatttt--ctgaaacttggcaaga--aggtttgatgaaattt--------ttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA

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|211318952|gb|FL142503.1|FL142503
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|71429669|gb|DR810719.1|DR810719
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|71441217|gb|DR822267.1|DR822267
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|91874947|gb|EB404904.1|EB404904
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|211318953|gb|FL142504.1|FL142504
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|93012917|gb|EB638437.1|EB638437
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
EST: gi|89251407|gb|DY623193.1|DY623193
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG                         GTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATC

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: 36 (upstream exon), 44 (downstream exon)
Score: 48

TTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 44

TTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 43

TTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 45

TTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGgtccatgtct ... ttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
                                       ccccatttattttc  CT-rich tract
                                           atttattttca  TA-rich tract