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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatccaacatcttgcatgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 1
-------------------CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc-caacatcttg-catgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag-----------------------------
                    |||  | |  |  |   |||  ||||||||||||||||||| ||||||| |||||||| ||||| || ||||||||| |||||||         |   ||| | | |        | | | ||||| ||   |   ||||  |||  |    ||  ||  | |     | | |                             
TTCCTTTCCTTGTTGGTAAGAGCAAGGCGAGACGTAACGTAATCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGACTGCGATCCCGCATGgtgagtagcggtggcgctttgtccttcacggccggtcgtgttgcgtgtgggctgtcgtgc--tgatgagccttttttttttctcccccgcccgactcccgtgctgttcgtacgtgttgccag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 2
CAGCTTGCCCTG-TAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatccaacatcttgcatgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag----------------------------
     |||  || |||||| | |||||||||||||||||||   ||||||| ||||| || ||||| || ||||| ||| |||||||   |||    |   |   ||   || |||     |  || || || ||||     | |    ||||  |     | ||| ||  |                             
----GTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTATCGGGGCCTCACCGCAGTCTCGAGACTGCGATCACGCATGgtgagtggtccg-tgtagcggtggcgctttgtcttcgtgtctgtgtgtatgtatgctgcttcaccggttgtgggggttgtcgtgctgatattttttccccgtgctgctcgtgttgccag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 3
-----CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatccaacatcttgcatgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag---------
     ||| |      ||||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| |||||||   |||        |  |  || | | ||    |   ||||       |||    |  | | || ||     || |||| |||  |         
CAGTGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttccgtttagcggtgtcgctttgtcct--tcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 2
--CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatccaacatcttgcatgcctattttctggcgatgcgtttgcatttatgtgcgctgaaaaattgttcgttgctttgtgttgtcag---------
  ||| |      ||||||| | ||||||||||||||||||||| ||||||| |||||||| |||||||| ||||||||| |||||||   |||        |  |  || | | ||    |   ||||       |||    |  | | || ||     || |||| |||  |         
TGCAGGTGCGGTGGTAGCCGAGCGCTCCGGCCATGGCGTTCTTCCGGGGCCTCACCGCGGTCTCGAGGCTGCGATCCCGCATGgtgagtgttccgtttagcggtgtcgctttgtcct--tcaccggtttagggggctgtcgtgttgatattttttttcccctctgtgctgttcgtgttgccag

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|58693317|gb|CK082004.1|CK082004
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: TGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     GCGTTCTTCAGTGGTGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: GCGTTCTTCAG-GG-GCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
EST: gi|58678175|gb|CK066862.1|CK066862
EST:     GATCCCGCGTG                         GCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC
genomic: GATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGC

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: 56 (upstream exon), 74 (downstream exon)
Score: 47

CAGCTTGCCCTGTAGCCGCGTGCTCCGGCCATGGCGTTCTTCAGGGGCCTGACCGCGGTGTCGAGGCTTCGATCCCGCGTGgtgagccatc ... gtgttgtcagGCACAGGAGGCCACCACGCTTGGTGGTGTGCGATGGCTGCAGATGCAGAGCGCATCTGATCTT




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