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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaaaatcaatcagcttgcctctgtaaactctttatgcaagtattttgttgtgattagccttcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 3
gtaaaacaaaatcaatcagcttgcctctgtaaa-ctctttatgcaagtattttg-ttgtgattagcc----ttcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
||||||||||  |      ||| | ||||| || |||||||||||||| ||||| |||||| |||      |  || || |||||||||||||| |||  |||| || ||| || | |||||| ||||||||| ||||||| ||||| |||||||| |||  |||| ||||||| |||
gtaaaacaaatcc------ctttcttctgtcaatctctttatgcaagtgttttggttgtgactagatcatatcattctgcagAAATCTGGAGAGTTAGTTACCAGTGTTGGGCTGAGTGCTGAGAATGAGATAATACACACCCTTGCTTTCTTAGCTGGTTCCATGGTTTGGTCGCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 3
gtaaaacaaaatcaatcagcttgcctctgtaaactctttatgcaagtattttg-ttgtgattagcct----tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
|||||||||| ||       |||  ||  | ||    || ||||||| || || |||||| | |  |      || || |||||||||||||| |||  ||||||| ||| || |||||||| ||||||||| ||||||| |||||||||||||| |||| |||| |||||||| ||
gtaaaacaaattcg------ttgattccatcaatctcttgtgcaagtgttgtggttgtgactggattagatctttctgcagAAATCTGGAGAGTTAGTTACCAATGTTGGGCTGAATGCTGAGAATGAGATAATACACACCCTTGCATTCTTAGCTGGTGCCATGGTTTGGTCAAAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 3
gtaaaacaaaatcaatcagcttgcc-tctgtaaactctttatg--caagtattttgttgtgattagccttcttttg----tagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
|| | |              ||    | |  |||| |||  |   ||| | |    |||  ||| |   ||| |||     ||||||| |||||  |    || |  |||||  | |||||||| ||||| ||||| || || ||||| |||||||||||  | |||||||||||||||
gtgagattttggtgtggtatttatgatgtacaaacccttctttgccaattgtaaaattgctatttgatgtctattgattacagAAATCAGGAGATTTTATGACAATAGCTGGTTTCAATGCTGAGAATGAAATACTGCATACCCTTGCCTTCTTAGCAGGGCTGATGATTTGGTCACAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaaaacaaaatcaat-cagcttgcctctgtaaactc---tttatgcaagtattttgttgtgattagccttctt-ttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
                ||  |  |  ||     |  | | || |   | |  |   |  || |||     ||||    ||| || || |   || ||||||| |||||  |   |      | |||| ||||||| || ||||||||||| || || ||||| |||||||| ||||| |||||||||||||||
gtaagtgaatgcatttgtggattatgataggcaccccctaccccccaacatacagatgcatacaaaataattgtgcccatttgctttgtgactgcagAAATCAGGAGACTTTCTAGTGGTAGTTGGCTTAAATGCAGAGAATGAGATACTGCATACCCTTGCGTTCTTAGCTGGTGTTATGATTTGGTCACAG

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|88392342|gb|CI612816.1|CI612816
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|88732275|gb|CI757123.1|CI757123
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCT
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCT
EST: gi|58671695|gb|CK060381.1|CK060381
EST:     TAATGGATACCACAACTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|88722297|gb|CI745807.1|CI745807
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAG
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAG
EST: gi|88737616|gb|CI761124.1|CI761124
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|88394689|gb|CI622563.1|CI622563
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|88760844|gb|CI770400.1|CI770400
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58678385|gb|CK067072.1|CK067072
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58678409|gb|CK067096.1|CK067096
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58686372|gb|CK075059.1|CK075059
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58683468|gb|CK072155.1|CK072155
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58664452|gb|CK053138.1|CK053138
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|88824982|gb|CI775547.1|CI775547
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58589625|gb|CF987933.1|CF987933
EST:     AAGTGGATACCACAATTCGGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: AA-TGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
EST: gi|58657010|gb|CK045690.1|CK045690
EST:     TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAG                         AAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA
genomic: TAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATA

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: 72 (upstream exon), 55 (downstream exon)
Score: 31

CAAATTCCATTTTATCCATGAAGCTGTAACTATATTAATGGATACCACAATTCTGTACTATAGAGTTCTTCCCTGGGTTTGGAAGgtaaaacaaa ... tcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctctgtaaactctttatgcaagtattttgttgtgattagccttcttttgtagAAATCTGGAGAGCTAGCAACCAATGCTGGCCTAAATGCTGAAAATGAGATACTACACACTCTTGCATTCTTAGCAGGTGTCATGATTTGGTCACAG
                                          ccttcttttgt  CT-rich tract
                      aagtatttt  TA-rich tract