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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgcagtattacgttattcaattaaaattcataggtttctacctctacatacttctaataaactgactttactaatctatcgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAACTTCAGTCTGTTTAATCTGCTAGAATTTTACCAATGCGTCATTTGTGCA

Basic information

species Oryza sativa
transcript LOC_Os01g54784.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54784.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G042099_T02 (Zea mays), 3'ss of exon 11
--------------gtacttgcagtattacgttattcaattaaaattc---ataggtttctacctct--acatacttctaataaactgactttacta-------atctatcga-----------------tgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAACTTCAG--TCTGTTTAATCTGCTAGAATTT-TACCAATGCGTCATTTGTGCA
                |     |  || |  ||||||||||  | | |   | | | |||||   ||  |||| ||||| | | |||||    |||        ||||    |                 | | |||||||||||||||||||| |||||||| ||||||||||| | ||    || || |||   |||| ||||| |||| | | |  ||||||  |||||        
gtactccagatatttcatccttaaaatgaaattattcaattctagtgctgaacatgattctagtgctgaacatgcttctcaaacactgatggcactgcattaggatctgctaaatatataaaaacctctctatgtagGCCCTCAAGTCAAGCCCAATTTAACCTGAAGACAAACCATCGACAGTGATACCTCACGTTCTGCTTAATGTGCTGGGACTAATACCAACACGTCAGGGTC---
















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|88958836|gb|CI381639.1|CI381639
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|29643216|gb|CB648223.1|CB648223
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|58692115|gb|CK080802.1|CK080802
EST:     CCCCTACACAGGATCCACAATGGAGGACTGNCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|58608266|gb|CK036299.1|CK036299
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|88510496|gb|CI438002.1|CI438002
EST:     TGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: TGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|88223323|gb|CI223172.1|CI223172
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|88486816|gb|CI424087.1|CI424087
EST:     AGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: AGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|29640875|gb|CB645882.1|CB645882
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|87021846|gb|CI278013.1|CI278013
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
EST: gi|396941229|gb|HO188438.1|HO188438
EST:     CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAG                         GCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA
genomic: CCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAA

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: 72 (upstream exon), 69 (downstream exon)
Score: 18

AGAAAGGCCCACACAATCAAGAGTTGTTATTTTGTTCAGGGATAGACCATCCCCTACACAGGATCCACAATGGAGGACTGCCGTTACATCCTCTAACAAGgtacttgcag ... cgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAACTTCAGTCTGTTTAATCTGCTAGAATTTTACCAATGCGTCATTTGTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctacctctacatacttctaataaactgactttactaatctatcgatgtatagGCCCTCAAGTCAAGCCCTATTTAACCAGAAGACAAACCGTTGATGTGGAAACTTCAGTCTGTTTAATCTGCTAGAATTTTACCAATGCGTCATTTGTGCA
                                  tactaat  putative branch site (score: 18)
             atacttctaataaa  TA-rich tract