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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctttctgtctttcttgtttcgattccatcttcaattctattctattcaattcatccaccaagcaatcgaatgaatcgaatcaaacaaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCTGAGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCG

Basic information

species Oryza sativa
transcript LOC_Os05g01250.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G092468_T01 (Zea mays), 3'ss of exon 1
gtttctttctgtctttcttgtttcgattccatcttcaattctattctattcaattcatccaccaagcaatcgaatgaatcgaatcaaacaaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCTGAGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCG
         |   | || |    | | | | |      ||  |||  ||   ||  ||||    || | || |   |||||| ||       || |||||||| |||| | |||||| |||| || || |||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||  | ||||||||||
--------gtacgtatcatcaaccaagttccttccttctttcattacat---atcaatccttgcag-attcaatcaaatcgattcctc----cctgcagATCACCAAGCGCGGCGACACCGTCGATGAAAAGATCAAGAAGCTCGACGCCGAGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCG
















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|88344647|gb|CI637256.1|CI637256
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88578356|gb|CI687279.1|CI687279
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCNACCGATCGG                         ATCAGNAAGAGGGGCGACTCCGTGGACGANAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|33655394|gb|CF278008.1|CF278008
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88436415|gb|CI691129.1|CI691129
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88406674|gb|CI603868.1|CI603868
EST:     AAGAAGAACCAGGAGCCCCCGCCCCAGCCATCCAGGATGCCACCGATCGG                         ATAAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: AAGAAGAACCAGGAGCCCCCG-CCCAG-CATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88327316|gb|CI645093.1|CI645093
EST:     CCCAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88589535|gb|CI705424.1|CI705424
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|66920747|gb|CX107595.1|CX107595
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|33662787|gb|CF293754.1|CF293754
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88425481|gb|CI567201.1|CI567201
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATGGG                         ATCAGCAAGAGGGGCGACTCCGTGGATGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88310981|gb|CI657894.1|CI657894
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|38483033|gb|CF966835.1|CF966835
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAACGATCAAGAAGCTGGACGC
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAA-GATCAAGAAGCTGGACGC
EST: gi|88331043|gb|CI638451.1|CI638451
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|87006073|gb|CI289490.1|CI289490
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|5003512|gb|AU068661.1|AU068661
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|33823135|gb|CF337370.1|CF337370
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|117224782|gb|CT845909.1|CT845909
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|88362605|gb|CI608754.1|CI608754
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
EST: gi|218491828|gb|FG966677.1|FG966677
EST:     CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGG                         ATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT
genomic: CCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCT

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), 66 (downstream exon)
Score: 10

CAATCGCCGCCTCCGCCTCCGATTCCTTCCGATGAAGAAGATCTTCGGCGCCAAGAAGAACCAGGAGCCCCCGCCCAGCATCCAGGATGCCACCGATCGGgtttctttct ... aaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCTGAGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattcaattcatccaccaagcaatcgaatgaatcgaatcaaacaaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCTGAGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCG
       aattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctttctgtctttcttgtttcgattccatcttcaattctattctattcaattcatccaccaagcaatcgaatgaatcgaatcaaacaaacccgcagATCAGCAAGAGGGGCGACTCCGTGGACGACAAGATCAAGAAGCTGGACGCTGAGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG