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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatgcagtaaaccaacttgttaaatgcattgtaatattttgtgcaaataatgtcttaagctgatgatctgtctatttctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG

Basic information

species Oryza sativa
transcript LOC_Os01g63870.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G095611_T01 (Zea mays), 3'ss of exon 5
gtgagtatgcagtaaaccaacttgttaaatgcattgtaatattttgtgcaaataatgtcttaagctgatgatctg-------tctattt---ctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
|||||||||||| ||| ||  || ||| |  || ||| ||||  ||   | |  |  | ||  |    |  ||||       |||||||    |||||||||||||||| ||| ||||| ||||||| ||| | |||||| | |||||||||
gtgagtatgcaggaaatca--tttttagacacaatgtgatataatgcaaataacacattttttgtcctttttctgaccattatctatttaacttgtgacagTACCTCCGGAAAATAAAGCTATTTGGGTACAGAGTGTTTCTTATTTATGCG
















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|58659627|gb|CK048307.1|CK048307
EST:     GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
EST: gi|58658393|gb|CK047073.1|CK047073
EST:     GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
EST: gi|58652789|gb|CK041469.1|CK041469
EST:     TATAGAGATGGGCCTATTACAATTATTGATTGTGGGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: TATAGAGATGGGCCTATTACAATTATTGATTGT-TGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
EST: gi|58654749|gb|CK043429.1|CK043429
EST:     GTATAGAGATGGGCCTATTACAATTA-TGATTGTTGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
EST: gi|58656604|gb|CK045284.1|CK045284
EST:     GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
EST: gi|58655477|gb|CK044157.1|CK044157
EST:     GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTA                         TACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
genomic: GTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG

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: 68 (upstream exon), 46 (downstream exon)
Score: 8

AGCTGTTGGACTTTCGTTTTTCAGTTATGGGTTCACTAAAGTAGGGTCATGTATAGAGATGGGCCTATTACAATTATTGATTGTTGTTATGTTTGCACTAgtgagtatgc ... tctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatattttgtgcaaataatgtcttaagctgatgatctgtctatttctgtgacagTACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG
                          agctgat  putative branch site (score: 8)
                                       tctatttct  putative PPT
             aaataatgtcttaa  TA-rich tract