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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaatccctttcttctgtcaatctctttatgcaagtgttttggttgtgactagatcatatcattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
gtaaaacaaatcc------ctttcttctgtcaatctctttatgcaagtgttttggttgtgactagatcatatcattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG
||||||||||  |      ||| | ||||| || |||||||||||||| ||||| |||||| |||      |  || || |||||||||||||| |||  |||| || ||| || | |||||| ||||||||| ||||||| ||||| |||||||| |||  |||| ||||||| |||
gtaaaacaaaatcaatcagcttgcctctgtaaa-ctctttatgcaagtattttg-ttgtgattagcc----ttcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
















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|211188255|gb|FL327236.1|FL327236
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|149101643|gb|EE187775.2|EE187775
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|71767568|gb|DR965505.1|DR965505
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211285085|gb|FL334458.1|FL334458
EST:     TAATGGATACTACNATACTATACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGGAGAGTTAG
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGG-AGAGTTAG
EST: gi|29130241|gb|CB380945.1|CB380945
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211469576|gb|FL315154.1|FL315154
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCT
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCT
EST: gi|76293281|gb|DV032849.1|DV032849
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|71446633|gb|DR827683.1|DR827683
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211337668|gb|FL335756.1|FL335756
EST:     AATGGATACTACCAATACTATACTATAGAGTTCTTCC-TGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGC
genomic: AATGGATACTAC-AATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGC
EST: gi|71330641|gb|DR802092.1|DR802092
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211481369|gb|FL368104.1|FL368104
EST:     AATGGATACTACRAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAGTGCTGA
genomic: AATGGATACTAC-AATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGA
EST: gi|211477296|gb|FL319649.1|FL319649
EST:     KAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AA-TCTGGAGAGTTAGTTTACCAGTGTTGGGCTGAGTG
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTT-ACCAGTGTTGGGCTGAGTG
EST: gi|78091217|gb|DV519591.1|DV519591
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211231531|gb|FL255915.1|FL255915
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211231534|gb|FL255918.1|FL255918
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211231535|gb|FL255919.1|FL255919
EST:     ACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: ACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211456968|gb|FL307879.1|FL307879
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|50322421|gb|CO517547.1|CO517547
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211023229|gb|FL319670.1|FL319670
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211274143|gb|FL330839.1|FL330839
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|78114998|gb|DV533386.1|DV533386
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|78113447|gb|DV531839.1|DV531839
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|50334362|gb|CO529488.1|CO529488
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|37424619|gb|CF650042.1|CF650042
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211203269|gb|FL344215.1|FL344215
EST:     TANTGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGA
EST: gi|211195422|gb|FL326474.1|FL326474
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTT
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTT
EST: gi|71436743|gb|DR817793.1|DR817793
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
EST: gi|211228866|gb|FL338409.1|FL338409
EST:     TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG                         AAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA
genomic: TAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATA

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: 178

CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 60

CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 121

CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAGgtaaaacaaa ... cattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaatctctttatgcaagtgttttggttgtgactagatcatatcattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG
                                            tcattct  CT-rich tract
                                         atatcatt  TA-rich tract