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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctcgacatgctatgattagtgaatcttaatattttgtattaccactgatattttttctttgctgttttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACTTGGTGTTGATGACCCAACTAAAATTCGGCTTACATCGCATAACTGTTAT

Basic information

species Oryza sativa
transcript LOC_Os07g06950.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 19
gtaagcatctcgacatgctatgattagtgaatcttaatattttgtattaccactgatattttttctttgctgt-tttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACTTGGTGTTGATGACCCAACTAAAATTCGGCTTACATCGCATAACTGTTAT
||||| || | |||||||| | || | | ||||| |||| | | | ||| | |||||||| | | ||| | |||||||| ||| |||||| |||||| |||| |||||||| || ||| |||||||||| || ||||||||| | ||||||||||||||||| ||||| ||||||
gtaagaatttggacatgctgt----agcagac--tgatattctgtactgctaatgaaaccttttcttttttttgtttttatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGGCTTACATCACATAATTGTTAT
















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|58661271|gb|CK049951.1|CK049951
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|66922652|gb|CX109500.1|CX109500
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58659867|gb|CK048547.1|CK048547
EST:     CATTTTCGTTCATTGGAGAAGCCCGGAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|27577375|gb|CB000070.1|CB000070
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTGACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58656552|gb|CK045232.1|CK045232
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58674203|gb|CK062889.1|CK062889
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58654004|gb|CK042684.1|CK042684
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|88410434|gb|CI686365.1|CI686365
EST:     GATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: GATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58658981|gb|CK047661.1|CK047661
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|58668010|gb|CK056696.1|CK056696
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
EST: gi|163920232|gb|EG710577.1|EG710577
EST:     CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGAT                         GTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT
genomic: CATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACT

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), 61 (downstream exon)
Score: 42

GTAGTCCATTTTCGTTCATTGGAGAAGCCCAAAGAGGATGATTTTTGTTTAGAGATgtaagcatct ... ttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACTTGGTGTTGATGACCCAACTAAAATTCGGCTTACATCGCATAACTGTTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttaatattttgtattaccactgatattttttctttgctgttttctgtatagGTCGAAGGCTTTCACGTATGATGAAGTAGTGGAAAAGGTGGCTCAAAAACTTGGTGTTGATGACCCAACTAAAATTCGGCTTACATCGCATAACTGTTAT
                     cactgat  putative branch site (score: 42)
 tattttttctttgctg  CT-rich tract
 taatattttgtatta  TA-rich tract