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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgtacttttggttttgtatttattatggctagcatatttatcaagattgatattgtgatgcattagcccctgagctgctactcaaattctaggt...

Basic information

species Oryza sativa
transcript LOC_Os04g59494.4
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G312026_T01 (Zea mays), 5'ss of exon 12
AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgtacttttggttttgtatttattatggctagcatatttatcaagattgatattgtgatgcattagcccctgagctgctactcaaattctaggt----
|||||| |||||  || |||| ||||||||||||||  ||||||| || |||||||| || |||||   ||| ||||| ||||||||||| |||||  |||| | |||||||| || |  |  | |  |  ||  |    | || |  || |    || |   |||   |   |      |   | |     |  | |      
AAATGTCTGGAACCTGCGGAAGTGTAGTGCTGCTGGGTTGGATGTTCTCTCTAATGTGTTTGGTGACAGCATCCTTCCAACTTTAATGCCATTGATTGAGgtgacttgtacttctgatagttaagtagtggtgctt--tttgttga--aaaacaagtactcaaatggcctgaactggagtcatttgcatggctcatggaaaaat

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 12
AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgtacttttggttttgtatttattatggctagcatatttatcaagattgatattgtgatgcattagcccctgagctgctactcaaattctag-gt-
|||||| |||||  || |||| ||||||||||||||  ||||||| || |||||||| || |||||   ||| ||||| ||||||||||| |||||  |||||| |||||| | ||||  | || | ||| |  ||    | || |  || |     | ||   || | | |  |||         ||||      |  || 
AAATGTCTGGAACCTGCGGAAGTGTAGTGCTGCTGGGTTGGATGTTCTCTCTAATGTGTTTGGTGACAGCATCCTTCCAACTTTAATGCCATTGATTGAGgtaacttgtacctatggtagtctagt-attgtttctt-tttgttgaaaaaaaacttaaatggcctgaactggagccttttgcatggctcatggaaaaacgtt

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 5'ss of exon 12
AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgtacttttggttttgtatttattatggctagcatatttatcaagattgatattgtgatgcattagcccctgagctgctactcaaattctaggt
||||  |||||||||| |||||||||||||||||||  | ||| |  | || |  || || || || || ||||| || | | | |||||| |  | ||||||  |  |  |  |  |  |  | ||        ||    ||||      ||||||||| | ||    | ||    || |  ||  |     | |||  
AAATTCTTGGAATTTGCGGAAATGTAGTGCTGCTGGATTAGATATATTATCAACAGTATTTGGGGACGATATTCTCCCAATTCTCATGCCTCTTGTGCAGgtacatccttgtcctactcgtagactt--------tactgaatttgc---aattgatattttcata---ttgcttacgaacacctgtt---gctgtag--

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S15_486V6.1 (Physcomitrella patens), 5'ss of exon 13
AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgtacttttggttttgtatttattatggctagcat--atttatcaagattgatattgtgatgcattagcccctgagctgctactcaaattctaggt
||||   ||||||||| ||||||||||||||||||| || ||| |  | || |  || || || ||||| ||||| || | | |  ||||  |  | ||||||      |  |||    |   |||| |||  ||    |   |    |||||  || | || |  |   || || | ||||  |||  |     | |||  
AAATTCGTGGAATTTGCGGAAATGTAGTGCTGCTGGACTAGATATATTATCAACAGTATTTGGGGATGAAATTCTCCCAATTCTTCTGCCCCTTGTGCAGgta-----catcttta---tccaatttcttacagcctttactgaaccgtcaag--tggtgtt-tactaggtt-gctcatgagtagctgtt---gctgtag--

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|33797567|gb|CF324643.1|CF324643
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|29624708|gb|CB629719.1|CB629719
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|33678128|gb|CF306367.1|CF306367
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58662574|gb|CK051260.1|CK051260
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58612862|gb|CK040574.1|CK040574
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     TAATGTTTTCGGTGATGACATTCTTGCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: TAATGTTTTCGGTGATGACATTCTT-CCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT

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 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 65 (downstream exon)
Score: 26

AAATGTTTGGAATTTGAGGAAATGTAGTGCTGCTGGCCTGGATGTCCTTTCTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC




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