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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattggcttttcttttcatgaacatcttatgctggagggtacaggaggtactgttatcaataatcatcatgtgcactccatttggtttctgtgtttacaaatgaagcatatgaattttgcatctgagagttaactcttgatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG

Basic information

species Oryza sativa
transcript LOC_Os03g55280.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55280.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 6
gtaattggcttttcttttcatgaacatcttatgctggagggtacaggaggtactgttatcaataatcatcatgtgcactccatt-tggtttctgtgtttacaaatgaagcatatgaattttgcatctg--agagttaactcttgatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG
       |  |||   ||||||  |||| | | |   ||    |   |   ||| ||  || | ||  ||||||  ||  || |   ||  | |     | || |  | |  |||| | ||  |      | |  |||| |    ||||||||||||| || |||||||| |||||||||||||| ||||||||||| ||||| |  |||| ||||  |||
-------gtattttggttcatgctcatcat-taccacag----ctataatcactattcacactcatt-tcatgtaaacagcagtgctgtcccggaagagaaaagttgatctaatgattattatactgagcaaaagtaacacactgtttttcagGTATCAGACAAAGATGACGTAGCAGTGGGTAGGATTCGTCAGGACTTGTCCCTGGATGGTAACCGAGG
















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|88245864|gb|CI245713.1|CI245713
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|86417412|gb|CI031621.1|CI031621
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|86482873|gb|CI125506.1|CI125506
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|87010136|gb|CI279233.1|CI279233
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|89186248|gb|CI262080.1|CI262080
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|5607365|gb|AU076037.1|AU076037
EST:     AATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: AATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|86258502|gb|CI064855.1|CI064855
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|41881827|gb|BX927612.1|BX927612
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|12404710|gb|AU166311.1|AU166311
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|86491066|gb|CI133699.1|CI133699
EST:     CCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: CCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|87029218|gb|CI276486.1|CI276486
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|13805857|gb|AU181226.1|AU181226
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
EST: gi|88974879|gb|CI023150.1|CI023150
EST:     TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAG                         GTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG
genomic: TTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCG

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: 70 (upstream exon), 68 (downstream exon)
Score: 37

GATACTGCAAGGGAAATCTTGAGGGCAGCTGAAGGTGTTACCATTATTGATGACCGTGCTTCCAATCGCTTCCCCACACCTCTTGAGgtaattggct ... gatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacaaatgaagcatatgaattttgcatctgagagttaactcttgatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG
                                               tttttc  CT-rich tract
              atatgaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattggcttttcttttcatgaacatcttatgctggagggtacaggaggtactgttatcaataatcatcatgtgcactccatttggtttctgtgtttacaaatgaagcatatgaattttgcatctgagagttaactcttgatttttcagGTATCGGATAAAGATGATGTAGCAGTGGGTAGAATTCGTCAGGATTTGTCGCAAGATGATAACAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG