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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTGAATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagtccacattctttttcggtgctgcaagcatattcctgtttctttgatggatttcagcatttttaatgcaaattccag

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G574782_T01 (Zea mays), 5'ss of exon 8
TGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTGAATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt-------ccacattctttttcggtgctgcaagcatattcctgtt-tctttgatggatttcagcatttttaat--gcaaattccag
||| || | || ||||||||||||||||||| |||| ||||| ||||||||||| ||||||||||||||| ||||||| || || ||||||||||| ||||||| |||||       |||||| |||  ||  |  |||||||||||   | || |||||| |  | |||||   || ||||  || || | |||
TGATGAGGGTGGCAAAGAAGAGGTTATCAATTCATTGGTTGCCAATGTTGAATCAATGATTAAAGCAGACCGGAAGATCACATCATTGAAACAACTTCAGgtagcttagtttgcaatccacatccttggtcacttttgcaagcatatgaattttatctttggtataattcagttgttctaattggccaaattcag
















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|86877415|gb|CI312773.1|CI312773
EST:     ATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: ATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|84117432|gb|CD151199.1|CD151199
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|25806482|gb|CA762443.1|CA762443
EST:     AATCGATGATTAAAGCAGACAGGAAGATTNNGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTN
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|33683942|gb|CF312181.1|CF312181
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGA
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGA
EST: gi|29686093|gb|CB682368.1|CB682368
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|4716001|gb|AU057117.1|AU057117
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|29671700|gb|CB667975.1|CB667975
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|11173109|gb|AU164617.1|AU164617
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACACCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|29615092|gb|CB620105.1|CB620105
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|427846|gb|D23987.1|D23987
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
EST: gi|58590134|gb|CF988442.1|CF988442
EST:     AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAG                         GGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT
genomic: AATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTT

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: 75 (upstream exon), 74 (downstream exon)
Score: 159

TGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTGAATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagt ... caaattccagGGCCACATATGGAGGACTGGTTTTGAAAGTAAAGAACTGCAAGGAGTTGTTTTCGATGATGTCCCCGAGGCGCTAAAGCACTGGCATGCTAGTGGCATGA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGATGCTGACAAAGAAGAGGTTATCAATGCATTAGTTGCTAATGTTGAATCGATGATTAAAGCAGACAGGAAGATTACGTCGTTGAAACAACTCCAGgtagattagtccacattctttttcggtgctgcaagcatattcctgtttctttgatggatttcagcatttttaatgcaaattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA