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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCCCACATGAACCCCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagatgcagcaacacagctacctcaaactgccaattcttcatatatattacttcttgcatcaaaatatatatgcaatataatagttagctatgtg...

Basic information

species Oryza sativa
transcript LOC_Os02g51110.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G028325_T02 (Zea mays), 5'ss of exon 2
GACGGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCCCACATGAACCCCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagatg--cagcaacacagctacctcaaactgccaattcttcatatatattactt---cttgcatcaaaatatatatgcaatataatagttagctatgtg
 || || ||||||||||||||||| |||||||| ||||| ||||||||||||||||| ||||||||||||||||||||| | |||||||||||||| |||||| ||    |  |           | | || ||   |  |  | |  | |  |||  ||   | | | |   ||  ||    |  |  | | |||  | ||   
CACCGTCATGATCTACGCCGTCGGACACATCTCGGGCGCGCACATGAACCCCGCCGTCACGCTCGCGTTCGCCGTGTTCCGCCATTTCCCCTGGATCCAGgtacgcgcccgtccgttcgtcttcttgcatcgaaactctgagccatagt-tgaattggttgggcatacgtactaacgtacgatcggtgcattcgttgac-at---

upper sequence: LOC_Os02g51110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G082184_T02 (Zea mays), 5'ss of exon 2
GACGGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCCCACATGAACCCCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagatgcagcaacacagctacctcaaactgccaattcttcatatatattacttcttgcatcaaaatatatatgcaatataatagttagctatgtg---
 || ||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||| | |||||||||||||| ||||||  |   | |    ||   |   |||     |||    ||   ||  | | |    | ||  |     | |      |  |      |    |   ||   
CACCGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCGCACATGAACCCCGCCGTCACGCTCGCCTTCGCCGTGTTCCGCCATTTCCCCTGGATCCAGgtacacgcgtccgcagacctggtctcctagctttgcg---tcgaaatcgaaactgagccatggctgggggtttgggcataggacggatatgcattcgttgaca

upper sequence: LOC_Os02g51110.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 2
GACGGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCCCACATGAACCCCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgc-agatgcagcaacacagctacc----tcaaactgccaatt---cttcatatatattacttcttgcatcaa--aatatatatgcaatataatagtta--gctatgtg------------------------------------------------
|| | | ||| |||||||||||||||||||||| || || |||||||| || |||||||| || ||||| ||     |  | ||||||||||||   || ||| || ||||    |  |     |  |    |  |   | | |||    |  || |  |||  | | || || |    ||   | | |  | |  |  ||   || || |                                                 
GATGATCATGGTCTACGCCGTCGGCCACATCTCTGGAGCTCACATGAATCCGGCCGTGACTCTGGCGTTTGCGACCGTGCGCCATTTCCCCTGGCAGCAAgtaagctagatctctcgcctagattctcgtgtttgagtggtcgattgagttagatttggattgat-cgtgaattagtcgatggttcttctttgtgttctttcccgcgatcttcgtcgctaactttggaagtgtttgattgaaatctctcctctctcccag

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|58606995|gb|CK035028.1|CK035028
EST:     CATTTCCCCTGGATTCAG                         GTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC
genomic: CATTTCCCCTGGATTCAGgtatgcagat ... ccttacacagGTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC
EST: gi|88761451|gb|CI771007.1|CI771007
EST:     CCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAG                         GTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC
genomic: CCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagat ... ccttacacagGTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC
EST: gi|25799107|gb|CA755068.1|CA755068
EST:     CCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAG                         GTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC
genomic: CCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagat ... ccttacacagGTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTC

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), 72 (downstream exon)
Score: 87

GACGGTGATGATCTACGCCGTCGGCCACATCTCCGGCGCCCACATGAACCCCGCCGTGACGCTCGCGTTCGCCGTGTTCAGGCATTTCCCCTGGATTCAGgtatgcagat ... ccttacacagGTTCCGTTCTACTGGGCGGCGCAGTTCACCGGAGCGATATGCGCGTCGTTCGTGCTCAAGGCGGTGATCCACCCGGTGGATGTGATCGGAACCACCACGC




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