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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatgccatccaaaccaaaaccatgtttgtggagggctattcttggtgcatttgttccgttttaacttctaatctgtttacttgtttcatgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTG

Basic information

species Oryza sativa
transcript LOC_Os03g50850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50850.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 2
acacatgccatccaaaccaa-aaccatgtttgtggagggctattcttggtgcatttgttccgttttaacttctaatctgtttacttgtttcatgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTG
  | | ||  | | |   || |   ||   | |    |   ||   | |||  | | ||   || | |  | | |  | | |  || || | || || ||||||||||| || ||| |||| || || |||||||| || |||||| |||||||||| |  |||||||| |||||||||||||| | ||||||||||||||
gaagaagctgtgctagtaaacagatattcatttatcagcaaatctctagtgtttctttttttttgtgaacttttaagtatat-tttattgcttgcttacagATCCGTGAATATCATCGGCGGAACCCATCTGCCCGCTTTGTTAGTACAACTGATGACTATGAAGAGCTTCTAAAGGAGGAACCAGTTATTGAATTCACTG
















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|29639903|gb|CB644912.1|CB644912
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|58663710|gb|CK052396.1|CK052396
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|86900664|gb|CI302081.1|CI302081
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTC
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTC
EST: gi|58654216|gb|CK042896.1|CK042896
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|117216922|gb|CT845265.1|CT845265
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|29625134|gb|CB630145.1|CB630145
EST:     CCACAGGGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|29675682|gb|CB671957.1|CB671957
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|58655319|gb|CK043999.1|CK043999
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|88393433|gb|CI618321.1|CI618321
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATC-GTGATTAGCATAGGGGTAATCCTTCTG
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTG
EST: gi|58669047|gb|CK057733.1|CK057733
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|58659954|gb|CK048634.1|CK048634
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|88363383|gb|CI643241.1|CI643241
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACT
EST: gi|88399904|gb|CI585823.1|CI585823
EST:     CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAG                         ATCCGTGATTACCATAGGCGTAATCCT
genomic: CCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCT

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: 74 (upstream exon), 61 (downstream exon)
Score: 29

CGAGGACAAGGATAATGCTAGGAAGGATGAGATCTCCAACCATCTTAGTTCCACAGTGCAAGCTGAAATCTTTCCAAAGTTCTATGACAGGCTCAAAGAGgtaatgatct ... atgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgcatttgttccgttttaacttctaatctgtttacttgtttcatgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTG
                       ttctaat  putative branch site (score: 29)
                ttttaacttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatgccatccaaaccaaaaccatgtttgtggagggctattcttggtgcatttgttccgttttaacttctaatctgtttacttgtttcatgtttgcagATCCGTGATTACCATAGGCGTAATCCTTCTGCCCGTTTCGTTAGTGCAACTGATGATTTCGAAGAGCTACTAAAGGAGGAACCGGCTATTGAATTCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA