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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtgatgcagtatagtgcttttgcacatttgaagttttctttcatgccgtacttcaattccttggttatttttttgtag

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 5'ss of exon 21
TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtgatgcagtatagtgcttttgcacatttgaagttttctttcatgccgtacttcaattccttggttatttttttgtag
|||  || | |||   ||||| | ||| ||||||||||||||||| ||||| |||| |||||| || ||||||||||||||||||||||||||||| ||||||| ||||||||||||  |||  |  ||    ||   |    ||  || |    | ||||  |||  | |              
TACGGCACCACTTTTATCAGTTCAGGCTCTGATTTTGCCTCCTAGCCATTTAAAAACGGAACTCTCATCAGTTCCTGATACTATTCCTCCAAGAGCACAGgtactaagtgatgcagtgcagttttaatgttttttcctaccgctcaatcctcattttcttccgttctgtag--------------
















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|211430870|gb|FL250418.1|FL250418
EST:     TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAG                         GTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
genomic: TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
EST: gi|71439223|gb|DR820273.1|DR820273
EST:     TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAG                         GTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
genomic: TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
EST: gi|40336758|gb|CK370828.1|CK370828
EST:     TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAG                         GTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
genomic: TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
EST: gi|38502665|gb|CF972525.1|CF972525
EST:     TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAG                         GTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
genomic: TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
EST: gi|211430871|gb|FL250419.1|FL250419
EST:     TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAG                         GTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG
genomic: TGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCG

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), 49 (downstream exon)
Score: 129

TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCGGTTCTAGATTTCTCGTATGCTTTTGGGACTTCACTG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 47

TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCGGTTCTAGATTTCTCGTATGCTTTTGGGACTTCACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 66

TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCGGTTCTAGATTTCTCGTATGCTTTTGGGACTTCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

TACTTCAGCCCTTACGTCAGTGCGGGCGCTGATTTTGCCTCCTAGTCATTTGAAAATGGAACTTTCGTCAGTTCCTGATACTATTCCTCCAAGAGCGCAGgtaccaagtg ... ttttttgtagGTGCAAGTTCCCCTTGAGGTTGCGAATCTCCTTGCAAGTAGAGATGTTGCGGTTCTAGATTTCTCGTATGCTTTTGGGACTTCACTG