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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtacttcttccagtattccacatgaacttgtattttgttaatgttggtaaggctgtttctttaaagtcagcttactgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG

Basic information

species Oryza sativa
transcript LOC_Os02g21250.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G314679_T04 (Zea mays), 3'ss of exon 4
gtattgtacttcttccagtattccacatgaacttgtattttgttaatgttggtaaggctgtttctttaaagtcagcttactgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG
   ||||   | |||   |||| |   || |  | ||||| |    |||   |  || |||||  | |    | |||||||||||||||||||||||||||||||| ||||||| || |||||  |||| ||||||||||||||||| ||||||||||| ||||| ||
--gttgtctattttctgttattac---tgcatatatattt-gcctttgt--atgtggttgttt--tgacgtgccgcttactgtgctttagGGGTGATGTTGAGAAGCGGACTGCGCTTGAGAACTTGGATTTGATACTTCTCTGCATTGATGAAATTGTGGATGGGGG
















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|88517568|gb|CI445222.1|CI445222
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|8955503|gb|BE229309.1|BE229309
EST:     TAGCAAATGTACTACAGGGCTTTTCGGATTCTGTTGTTCTTTAAATTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTC
genomic: TAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTT-TACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTC
EST: gi|86506579|gb|CI149212.1|CI149212
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88281898|gb|CI403294.1|CI403294
EST:     TCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: TCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|86831266|gb|CI297535.1|CI297535
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|86526502|gb|CI166708.1|CI166708
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88511151|gb|CI438657.1|CI438657
EST:     CTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: CTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|163928617|gb|EG711178.1|EG711178
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88520651|gb|CI448305.1|CI448305
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88243238|gb|CI244360.1|CI244360
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88483987|gb|CI421258.1|CI421258
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|86522432|gb|CI162638.1|CI162638
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|117248583|gb|CT862782.1|CT862782
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|163927524|gb|EG709956.1|EG709956
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88964103|gb|CI033020.1|CI033020
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
EST: gi|88491507|gb|CI428779.1|CI428779
EST:     ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAG                         GGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT
genomic: ATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCT

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), 75 (downstream exon)
Score: 34

AAGACCTTCATTTTTTTGTCACCGCTGGTGATGATGAGAATGAGCTCATTATAGCAAATGTACTACAGGGCTTCTCTGATTCTGTTGGTCTTTTACTCAGgtattgtact ... tgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgttaatgttggtaaggctgtttctttaaagtcagcttactgtgctttagGGGTGATGTTGAGAAGAGGACTGCACTCGAGAATCTGGACTTGATACTTCTCTGCATCGATGAAATTGTAGATGGCGG
                                      agcttac  putative branch site (score: 34)
                         tttctttaaa  TA-rich tract