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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggacatctttaaaatccatttctctttctgattttctttaatattattgtgtggctgataatatatcggtatggatgctgtgatggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGAGATGAGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTT

Basic information

species Oryza sativa
transcript LOC_Os09g34910.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G164956_T02 (Zea mays), 3'ss of exon 5
gtgcggacatctttaaaatccatttctctttctgattttctttaatattattgtgtggctgataatatatcggtatggatgctgtgatggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGAGATGAGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTT
||  |  |||||| | |   | | ||| |||   || || ||  |   | |||||  ||||| ||| |   | | ||||       ||  || ||||||||  |||| ||||| |||  ||  | |||||| ||||||||||| ||  | |||||| |||| || ||||||||||||| ||| |||||||||||||
gtaagaccatctt-atatgacttctctattttaaatatttttccagtgttttgtg-agctgaaaatgt---gatctgga-------attattgtagCTCTCTATGAGGTTTCTGAAAGTTGACAGGAAAACAGTTGATCTTGTCGGTAACGAGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTT

upper sequence: LOC_Os09g34910.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G149520_T02 (Zea mays), 3'ss of exon 5
gtgcggacatctttaaaatccatttctctttctgattttctttaa--tattattgtgtggctgataatatatcggtatggatgctgtgatggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGAGATGAGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTT
||  |  ||| ||  |   |  |     |||   || || |||    |||| |||||  ||||| |||   | | | ||||       ||  || ||||||||  |||| ||||| |||  ||  | |||||| ||||||||||| ||  |||||||| |||| || ||||||||||||| ||| |||||||||||||
gtaagatcattttataggactttcatatttttaaatattttttggactatttttgtg-agctgacaat---ttgatttgga-------attattgtagCTCTCTATGAGGTTTCTGAAAGTTGACAGGAAAACAGTTGATCTTGTCGGTAATGAGAAACTGAAGGCCAGTGCATCTGTTAAGCACCTTGCTCTTCCTT
















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|218492687|gb|FG950734.1|FG950734
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAAACGGTTGATCTTGTTGG
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAA-CGGTTGATCTTGTTGG
EST: gi|218497043|gb|FG966022.1|FG966022
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
EST: gi|29679593|gb|CB675868.1|CB675868
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
EST: gi|29628388|gb|CB633399.1|CB633399
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
EST: gi|25802299|gb|CA758260.1|CA758260
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
EST: gi|29637932|gb|CB642941.1|CB642941
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
EST: gi|58691703|gb|CK080390.1|CK080390
EST:     AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAG                         CTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA
genomic: AAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGA

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: 53 (upstream exon), 74 (downstream exon)
Score: 56

GCAAAGTTGAAGATGTTACAAAAGTACAGACACTTCTCTTCAGCGCTACTATACCAGAGTGGGTGAAGAAGgtgcggacat ... atggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGAGATGAGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatattattgtgtggctgataatatatcggtatggatgctgtgatggttatagCTCTCCTTGAGATTTCTCAAATCTGGAAAGAAAACGGTTGATCTTGTTGGAGATGAGAAATTGAAAGCTAGTGCATCTGTTAGGCATCTTGCTCTTCCTT
               ggctgat  putative branch site (score: 56)
                  tgataatatat  TA-rich tract