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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtttgggttctaggcctccctagtccctacacaagttgatgtttcaaatcttgaaatttcttactcgtactaggatttgcttctaaggaaaatgctcgtacttttatcaccgtcatcatgatcgtcatttcacggttgatctgtacag

Basic information

species Zea mays
transcript GRMZM2G471805_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g57330.1 (Oryza sativa), 5'ss of exon 3
GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtttgggttctaggcctccctagtc--cctacacaagttgatgtttcaaatcttgaaatttcttactcgtactaggatttgcttctaag-gaaaatgctcgtacttttatcaccgtcatcatgatcgtcatttcacggttgatctgtacag
||||| ||||| |||||||| || |||||||||||||||||||| |||||||| |||||||||||||||||   ||    |  | || || |  ||    |||  ||||||||| |   || ||    |||| |  || || | | |     ||   |||   |   ||||||                                                   
GATCCTAACTCGAAGCACCTCGGAACCACGGTCTGGGATGCATCCATGGTGTTCGTCAAGTTCTTGgtaatctcttc---tctttggactactgagctatcctgtacaagttgaag---cagat----aaatgtgataatcatgcaaattgctggaactattcggtgatgctccct------------------------------------------------

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G08490.1 (Glycine max), 5'ss of exon 4
GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtttgggttctaggcctccctagtccctaca--caagttgatgtttcaaatcttgaaatttcttactcgtactaggatttgcttctaaggaaaatgctcgtacttttatcaccgtcatcatgatcgtcatttcacggttgatctgtacag
||||| || ||||||||| | ||||| || || |||||||||||| | ||||||||||||||  | ||||   || ||      |      | |  ||   |    |  |||  | |||  |    ||  |    ||| | |  |     | |  || || | ||                                                          
GATCCCAATTCCAAGCACTTAGGGACTACAGTATGGGATGCATCACTTGTGTTTGTCAAGTTTCTTgtaagctgtgtgctcctcacaatcacatgctctggaatgtcctgttactcttttcatgaatgcgaaagtttattagaccctaagtgtatttttacgtaac---------------------------------------------------------
















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|211243538|gb|FL421850.1|FL421850
EST:     ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTG                         GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG
genomic: ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG
EST: gi|60395803|gb|DN228673.1|DN228673
EST:     ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTG                         GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG
genomic: ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG
EST: gi|211019758|gb|FL395380.1|FL395380
EST:     ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTBAAGTTCTTG                         GAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG
genomic: ACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAG

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: 125

GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 40

GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 22

GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GATCCAAACTCCAAGCACCTTGGGACCACGGTCTGGGATGCATCAATGGTGTTTGTCAAGTTCTTGgtaattggtt ... atctgtacagGAAAAGAATAGCAGAAAAGGTCGGTTTTGTCCATCCAAGCTAAAAGGAAAGAGAGTGATTGAATTAGGAGCTGGCTGTGGCCTGGCTGGGTTCG