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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattgtacctcgatctattttaaactaaccaatgcttccttttatcaagccatacttgagtaa...

Basic information

species Oryza sativa
transcript LOC_Os03g55890.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G843914_T03 (Zea mays), 5'ss of exon 10
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaatt-ggtgtcatcttcattgtacctcgatctatt-ttaaactaaccaatgcttcctttta---tcaa-gccata-cttgagtaa-
 ||| ||||||  ||||||| |||||  |||||||||||||| ||| | ||||||||||||||||||||||||||||| || ||||||||||||||||||||||||  |    | |   |  | || |||||      ||||||||||   | | || |||||| |||  |    ||  | |    |||  |||  |  |||||||  
GGTGAGCAAAGCGGGGCATGAGTGGCGGGCCTTTGCCGTTGCGCAACCGGAGCCTCTTTTACGCTTTGCGCTTTGTTCCGGCAGCCATTCTGATCCCGCGgtaagc--aacaagctccgtagactttggtgt------cattgtacctgagtatcttcttaaacaaacttagaagtcagtatggggtcagtgcctcagtttgagtaca

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G052476_T04 (Zea mays), 5'ss of exon 7
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattgtacctcgatctattttaaactaaccaatgcttccttttatcaag--ccatacttgagtaa
|||| ||||||  ||||||| ||||| |||||||||||| |||||| | ||||||||||| |||||||||||||| || || ||||||||||||||||||||||||  |     ||  |   |   |  |   || |      |   | |    ||   ||        |    | |  | | | |   |  ||     |  
AGTGAGCAAAGCGGGGCATGAGTGGCGAGCCTTTGCCGTCGCACAACCGGAGCCTCTTTTGCGCTTTGCGCTTTGCTCCGGCAGCCATTCTGATCCCGCGgtaagc--aacaatttcccaagacccgcaggtgtcgttgcatcaaagcaacaagttccgaatcttttcgtctgccatcatgttaggaatctcacgctgttgc

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA01G38680.1 (Glycine max), 5'ss of exon 12
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattgtacctcgatctattttaaactaaccaatgcttcct-tttatcaagcca--tacttgagtaa
|     |||||  ||  ||    | ||||||| |||  | |  ||| | || ||||||| || |||||| || |||||||||| |||||||||||| ||||||   ||  |   || ||        |     || | | |  |  |      |  || |    |  |||  ||  | ||| |   | ||  | |||    | 
AAAATTCAAAGCTGGAGATAGACGACAAGCCTATGCACTGGAGCAAGCTGAACCTCTTTCACACTTTGCACTCTGTTCAGGAAACCATTCTGATCCTGCGgta--ttccctcaattctcattggcgagcaatttcgttact-cattttcgcaaagcttgattatatgaataatttatatttgtttgggcaattccttatacat

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA02G06790.1 (Glycine max), 5'ss of exon 10
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattgtacctcgatctat---tttaaactaaccaatgcttccttttatcaagccatacttgagtaa
|     |||||  ||  |||   | ||||| |   |  |||  |   | ||||||||| ||| |||||| || |||||||||| |||||||||||| ||||||      ||   | |||||    || |   || |   || |   | ||  | |   ||  |||    | ||  |||  |   | ||    |  ||  |   
AAAATTCAAAGCTGGAGATGGACGACAAGCATACCCGATTGAGCGTCCTGAGCCTCTTCTACACTTTGCACTCTGTTCAGGAAACCATTCTGATCCAGCGgtacttatttttactcttctctgtgtgtttgtatgtgatttttcattagacttgtaagttgtaacgtctccatttttcaatgctttaacattttttttgg---

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA11G12930.1 (Glycine max), 5'ss of exon 8
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattg-tacctcgatctattttaaactaaccaatgcttccttttatcaagccatacttgagtaa---
|      || ||  |  |||   |  |||  | |||  |    |   |||| ||| | |||| |||||| || || |||||||||||||||||||| ||||||  ||  | |  | || |   | |  | |||| ||  |   |      || || | | |   |   ||||        ||| ||     ||   | |||   
AAAACCAAAGGTTAGAGATGCAAGAAAAGGATATGCTATACATCGTCCAGAACCTTTATTACTCTTTGCTCTATGCTCAGGAAGCCATTCTGATCCTGCGgtagacttctgg--tctttttgtacttatttcatatttgtcaatgttgatatgtactctgatacatataatgaaagaaaatatgaaata--acggaactaattt

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA11G06610.1 (Glycine max), 5'ss of exon 6
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcattgtacctcgatctattttaaactaaccaatgctt--ccttttatcaagccatacttgagtaa-
|     |||||  ||  ||    | ||||||| |||  | |  ||| | |||||||||| || |||||| || |||||||||| |||||||||||| ||||||   ||  |   || ||     |  |     || | | |  |  |      |  || |    |  |||  ||    |||  |   || || | | |   | 
AAAATTCAAAGCTGGAGATAGACGACAAGCCTATGCACTGGAGCAAGCTGAGCCTCTTTCACACTTTGCACTCTGTTCAGGAAACCATTCTGATCCTGCGgta--ttcccttaattctcatgggtgtgcaatttcgttact-catttttgcaaagcttgattatatgaataattgatatttgtttgggcaattccttatacat

upper sequence: LOC_Os03g55890.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA12G05060.1 (Glycine max), 5'ss of exon 11
AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcattgcgttttctcaaattggtgtcatcttcat-tgtacctcgatctat---tttaaactaaccaa--tgcttccttttatcaagccatacttgagtaa
|      || ||  |  |||   |  |||  | |||| |    |   |||||||| | ||||  ||||| ||||| |||||||||||||||||||| ||||||  ||  | |  | ||   | | |  | ||||  |||| | |  ||   |  |    | |  || |||| |  |  ||  || |||  |||  | ||       
AAAACCAAAGGTTAGAGATGCAAGAAAAGGATATGCCATACATCGTCCAGAGCCTTTATTACTATTTGCTCTTTGCTCAGGAAGCCATTCTGATCCTGCGgtagacttctgg--tctttctatacttatttcataatcatatttgactatgtagaaggatatgtacaaacctacatattttgttctatttagctcttctccg----

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|86481461|gb|CI124094.1|CI124094
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCG                         GTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcat ... ttttctgcagGTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAG
EST: gi|163927767|gb|EG712503.1|EG712503
EST:     AGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCG                         GTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAG
genomic: AGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcat ... ttttctgcagGTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAG

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: 61 (upstream exon), 30 (downstream exon)
Score: 5

AGTGGGCAAAGTAGGGCATGTGTGGCAAGCCTTTGCCGTTGCACAATCAGAGCCTCTTTTACGCTTTGCGCTTTGTTCAGGAAGCCATTCTGATCCCGCGgtaagctcat ... ttttctgcagGTGAGAGTGTACACTCCAAAGAGGCTGTTCCATCAACTGGAGGCTGCCAAGGAGGAGTTCATCCGGGCAACGGTGGGCATCTGGAAGGAGCAGAAAATAC




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