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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgtatgtcaatcattacttgcatttgtttgatcaggctataatgctaactggatttcactttatggtaatttgcaccttttacccccag

Basic information

species Zea mays
transcript GRMZM2G119749_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119749_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g15660.1 (Oryza sativa), 5'ss of exon 3
CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgtatgtcaatcattacttgcatttgtttgatcaggctataatgctaactggatttcactttatggt-----aatttgcaccttttacccccag
 |||  |||| | |    ||| | | | |||||||| |||||||||||||| ||||||||||| ||| |||||||||||||| ||| |   |   |  ||  |  ||   ||| |||     || ||| | | ||  |||| || | ||  |     |||||||| ||  || |  |||
TCTGACAAATCTCCGGTCTTTGCAAGATGCAACTCATTTGCTCATCTCCATTCCACCCATCCCGGGAATTGGTGATCCTgtacgttctcaattgcttgttgatgtca---gttcgattgactta-aattccatctaaatttaacataataatgattaaatttgcatctaatatctacag
















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|148943933|gb|EC889013.2|EC889013
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
EST: gi|28873904|gb|CB329832.1|CB329832
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
EST: gi|211402888|gb|FL264439.1|FL264439
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTG
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTG
EST: gi|211402891|gb|FL264442.1|FL264442
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
EST: gi|50325557|gb|CO520683.1|CO520683
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
EST: gi|148989559|gb|EE031740.2|EE031740
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
EST: gi|91878058|gb|EB408015.1|EB408015
EST:     CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCT                         CTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT
genomic: CAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAAT

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: 42 (upstream exon), 47 (downstream exon)
Score: 26

CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAATCTTGAATGGCTATGCTACCTTTCGTCAACAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAATCTTGAATGGCTATGCTACCTTTCGTCAACAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 29

CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAATCTTGAATGGCTATGCTACCTTTCGTCAACAA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 23

CCTGGAAAATATTCACAGTTTACGACAAGCAACTCACTTGCTCATCTCCATCCCACCCATCCCTGGAGTTGGTGATCCTgtaagttgta ... ttacccccagCTACTTATTAATTTAGATGAAGATCTGAGGAGAATACTCGGCCATGGTAATCTTGAATGGCTATGCTACCTTTCGTCAACAA