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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgacatttcaggtttagcactagaaaaaacagtgagcttcgtacaacacaaattgacatgatacccctcctttggtttcag

Basic information

species Oryza sativa
transcript LOC_Os10g38980.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38980.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G162251_T02 (Zea mays), 5'ss of exon 5
AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggt--gacatttcaggtttagcactagaaaaaacagtgagcttcgtacaacacaaattgacatgataccc-ctcctttggtttcag-------------------------------------------------
|| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||||    | ||||  |  ||  |    | ||| || |     |    | | | | ||    ||||||| | | ||  |||                                                         
AACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCCATCCTCATCTTCTGTCCAATCATTGTCACTTTGTGCTCCAGgtaagagcaggcattctaatttgggtcacaaaaacaatacactacaattttcgaaataa--caacatgattctcactatttttaacatgttgagtactagtttttgtctaatcacattggcatcctcttttggattcag

upper sequence: LOC_Os10g38980.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA09G36130.1 (Glycine max), 5'ss of exon 5
AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTG---TTCAATCCTTGTCACTTTGTGCTCCAGgtaag-gt---gacatttcaggtttagcactagaaaaaacagtgagcttcgtacaacacaa-attgacatgatacccctcctt--tggtttcag--------------------------------
    |  | ||| |||| |||||||||||||||||||| |||||||| ||||| ||||| || |||||||||    ||  |||  ||||||| ||||| || |||| | ||   ||||  |  | |||  |   |               ||  | ||  |      |   ||||||   |    |  || || ||                                 
---TCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCCTTCTTCATCATCTTCATTTGCATCTATGTCACTCTGTGCACCTGgtatgtgtttggacaaatttgctttctcttgatcgctgcttactttttttattcaggatgttggtattatgatattacaaaatactgtttgcatatgcttaactcttgtctctatttttttttcag

upper sequence: LOC_Os10g38980.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA12G01200.1 (Glycine max), 5'ss of exon 6
AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTG---TTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgacatttcaggtttagcactagaaaaaacagtgagcttcgtacaacacaaat-----tgacatgatacccc--tcctttggtttcag---------------------------------
    |  | ||| |||| |||||||||||||||||||| |||||||| || || ||||| || |||||||||    ||  |||  ||||||| ||||| || |||| |          | |||     ||    |   | |    |||  |  |   |  ||     |   ||||||   |  |    || || ||                                  
---TCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCCTTCTTCATCATCTTCATTTGCATCTATGTCACTCTGTGCACCTGgtatgtgtttggacaaagttggtttctcttgatcgctgcttacttttttaattccggatgttggtattatgatagtacaatatactgtttgcatttgcttgacttgtctctatttttttttttgcag

upper sequence: LOC_Os10g38980.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G30700.1 (Arabidopsis thaliana), 5'ss of exon 6
AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaa------------------ggtgacatttcag-----gtttagcactagaaaaaacagtgagcttcgtacaacacaaattgacatgatacccctcctttggtttcag-------------
||  |  | |||   || ||||||||||||||||  ||||||||||| || ||||||||||| ||||| ||  |    || ||||| || |||||||| |||||                  | |  | | | |      |||      |  | |||||    |  ||   |   || |||  |   || |    ||  ||   ||| |              
AACACATCAGGCTACAGCTTTACATGTGATTTGACAGACAACATTGCTGCTCCATGGCCATCTTCATCGTCAATGTCTTCTTTGTCTCTATGTGCTCCTGgtaatcacttctctctctacctgttctcttcttactcattgttggagcttccagaaaactaaaaagtttaaattgcaaaaaaagttttgctttatcttattcaattttattttaaatatgcag

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|86500464|gb|CI143097.1|CI143097
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
EST: gi|116875026|gb|EC365534.1|EC365534
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
EST: gi|29666973|gb|CB663248.1|CB663248
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
EST: gi|86504223|gb|CI146856.1|CI146856
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|86861783|gb|CI329548.1|CI329548
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|88522672|gb|CI449489.1|CI449489
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|88555527|gb|CI485792.1|CI485792
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|88466556|gb|CI532363.1|CI532363
EST:     GCCGTGNCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|88522247|gb|CI449992.1|CI449992
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|88552657|gb|CI482685.1|CI482685
EST:     CCATGGCCATCATCATCATCGGTTCAATCCTTGTCACTTTGTGGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGCTCAGT
genomic: CCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGT-GCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAA-GCTC---
EST: gi|88537263|gb|CI465088.1|CI465088
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG
EST: gi|116875033|gb|EC365541.1|EC365541
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
EST: gi|29640850|gb|CB645857.1|CB645857
EST:     GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
genomic: GCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG
EST: gi|88483086|gb|CI420357.1|CI420357
EST:     TCACTTTGTGCTCCAG                         AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGTAG
genomic: TCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTC---AG

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: 37 (upstream exon), 25 (downstream exon)
Score: 3

AATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCCATCATCATCATCTGTTCAATCCTTGTCACTTTGTGCTCCAGgtaaggtgac ... ttggtttcagAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG




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