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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag...

Basic information

species Oryza sativa
transcript LOC_Os09g34040.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G142806_T01 (Zea mays), 5'ss of exon 8
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag---
|| ||||| || ||||| ||||| || |||||||||||||| |||||||||||||||||||| |||||  | ||||| ||||| |||| ||||||||| ||||||||||| |  || | | | | | |  || | |  | | | |  | |   |   ||  |   || ||    |  |    | | |  |  |||        
TCGAAGTTCCTTGATGGAATGCAGGATCATTACACCTTTGCGCAACCAGGAATTCAGCGCCTCGTTTTTCGATTGAAGGAACTAGTTCGTCGTATAGACGgtaatgttccactgatccca-tctgtctacacttatggtttcgttccactctgaagcacaaatgtaatggctgttccat--ctcaaataataattgtggtggg

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G42180.1 (Glycine max), 5'ss of exon 7
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctc-caattcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaa----ggatttagaggactattacaag
|||||||| || ||  |||||||||||||||| || ||||||||||||||||||||  | |||||||| | |||||| ||| | ||     | || || |||||  ||  || ||   |   | ||| |   | |    |||  ||| ||||  ||  | | |||||        || |    |||||| ||     ||||    
TCAAAGTTGCTTGACAGTATGCAAGACCATTATACATTTGCTCAACCAGGAATTCAAAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGACGgtaacttttttctcaggcctgttgttttt---cttcaagtatatctataattgcatgaatttaaagaccccacttttgaatatggatttggatatgcattaat--

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA11G13330.1 (Glycine max), 5'ss of exon 7
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctagaattatat---ctactgaaagaaagggaactta--aggatttagaggactattacaag-----
|||||||| || ||||||||||||||||||||||| || |||||||| ||||||||| | |||||||| | |||||| ||| | ||     | || ||||||||   |  || ||     | ||||       |||| |  | | || ||| |||    |  |||||   |     ||||  |   ||||  |   |  ||| |      
TCAAAGTTGCTTGATGGTATGCAAGACCATTACACATTCGCTCAACCTGGAATTCAGAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacacttttctaa---ggacattt-------tgttttcctccaagcattgtataattttatgaaatttaaatgccttactattttttattgatttgataccattttta

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G05350.1 (Glycine max), 5'ss of exon 8
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaa---ttcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag
|||||||| || ||||||||||||||||||||||| || |||||||| ||||||||| | |||||||| | |||||| ||| | ||     | || ||||||||  ||  || ||    |    | ||  |  |    || ||| | |  | | | || ||        |       |||  ||||| |   || ||| | | 
TCAAAGTTGCTTGATGGTATGCAAGACCATTACACATTCGCTCAACCTGGAATTCAGAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacctttttctaaggccttttgttttcctccaagcattgtatagtttta-tgaaatttaaatgcctcactattttttattgatttggt--accatttctat

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G03200.1 (Glycine max), 5'ss of exon 7
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag-----
|||||||| || |||||||||||||||||||| || ||||| ||||||||||||||  | |||||||| | |||||| ||| | ||     | || ||||||||  ||  ||   | |  |   | |      | ||       || || || || |    |||  |      |        |||  |  || |   |       
TCAAAGTTGCTTGATGGTATGCAAGACCATTATACGTTTGCCCAACCAGGAATTCAAAGGCTTGTTTTTAAGTTGAAGGAATTGGTCAGGAGGATTGATGgtaacttttttctcttaccgaacctcag-----ttttaggaaaatataactacatttggctaaattattctctcactctatattaatgctctctcttatttcaca

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 5'ss of exon 7
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctag-aattatatctactgaaagaaagggaacttaaggatttagaggactattacaag--
 ||||| | || || ||||||||||| |||||||| ||||||||||| ||||| ||| | ||||| || | | |||| ||||| ||    ||||| |||||||   |    | |  |    |   | | ||   | | | |   | |  ||| | |   || |  || | | |  |       ||| || |  ||   ||   
ACAAAGCTCCTTGACGGTATGCAAGATCATTACACGTTTGCTCAACCTGGAATCCAGAGACTTGTGTTTAAGCTGAAGGAACTGGTCAGGCGTATCGATGgtaggttcttgctagcttg--ttcctgttaattggatgtgtctttggtgattgtttgagcttat-gacatgcacgtcctctccttacagaatcatgttaatta

upper sequence: LOC_Os09g34040.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 5'ss of exon 7
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaa--tgttcctccaat--tcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag
|||||||| ||||||||||||||||||||||| || ||||||||||||||||| ||  | || || || | | |||| ||| | || |  || || |||||||     ||    | ||  ||||  |  | |    ||||| | |    |  ||||  |  |   |        ||| |  ||     | || |  | || |  
TCAAAGTTGCTCGATGGTATGCAAGACCATTATACATTTGCTCAACCAGGAATACAAAGACTCGTGTTTAAGCTGAAGGAATTGGTCCGACGGATTGATGgtatgcccttttgtcgatgatcaaggaaatttattgctgtttt-tcatcaatattactttcaacaattttccaagaaat--agttcagaaagaataactaaac-

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|88961123|gb|CI096526.1|CI096526
EST:     AAAGAACTTGTTCATCGTATAGATG                         AACCTGTGTCAAAGCACATGGAGGAACTAGGATTGGACTTTCTTCAGTGTG
genomic: AAAGAACTTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
EST: gi|86501940|gb|CI144573.1|CI144573
EST:     AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATG                         AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
genomic: AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
EST: gi|86493863|gb|CI136496.1|CI136496
EST:     AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATG                         AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
genomic: AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
EST: gi|7332463|gb|AU085809.1|AU085809
EST:     TCAGCGCCTTNGTTTTCAGGTGGAAAGAACTTGTTGCATCCGTATAGATG                         AACCCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTT
genomic: TCAGCGCCTT-GTTTTCAGGTTGAAAGAACTTGTT-CAT-CGTATAGATGgtaatgttcc ... ggttatacagAA-CCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTT
EST: gi|88223252|gb|CI223101.1|CI223101
EST:     TTGTTCATCGTATAGATG                         AACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
genomic: TTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
EST: gi|38479672|gb|CF963761.1|CF963761
EST:     ATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATACGTATAGATG                         AACCTGTTTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
genomic: ATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCAT-CGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
EST: gi|27547564|gb|CA767379.2|CA767379
EST:     AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATG                         AACCTGTTTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG
genomic: AATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTG

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), 67 (downstream exon)
Score: 19

TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcc ... ggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAGTTTCTCGATGGTATGCAAGACCATTACACCTTTGCTCAACCAGGAATTCAGCGCCTTGTTTTCAGGTTGAAAGAACTTGTTCATCGTATAGATGgtaatgttcctccaattcaaatatttatgaacctgttctattgctagaattatatctactgaaagaaagggaacttaaggatttagaggactattacaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa