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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgattttgttgcatgttcaattacaaccttttcattatgttgtaccacatcattgttctataatgaagttatagaactttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g69130.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 9
gttcgtgattttgttgcatgttcaattacaaccttttcattatgttgtaccacatcattgttctataatgaagttatagaactttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG
              ||| |        |     ||||||| || |  |   | | | ||||   |  |     ||| | |  | |    |||||| ||||| |||||||| |||||||| |||||||| ||||| |||||||| || || |||||||||||||| |||||| |||| |||||||| 
-------------gtgcgtaactggacagtgg-ttttcatcatatgttgata-agcgttgt--cacgagtctattaaatatatatcattacagGAGGTTGATCCTTGTGAGGATGTTACAGATGAAGATATCCGCATGGCTATTCAAAATGCAACTGGTCCTAGAAGTGCTCTGTTTGTACCTGAA

upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G180335_T03 (Zea mays), 3'ss of exon 1
gttcgtgattttgttgcatgttcaattacaaccttttcattatgttgtaccacatcattgttctataatgaagttatagaactttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG
                  || | ||   ||   || |  | ||  |     | |   || |   || |  |  | | | |  | | | ||||||| ||||| ||||| || |||||||| || | ||| ||||| |||||||| || || |||||||||||||| |||||| |||| |||||||| 
-----------------gtgcttaaccgcacagttgttttcattatacgtta-agtgttat--catgagtatatgaaatatatgtcttcacagGAGGTTGATCCTTGCGAGGATGTTACAGACGTAGATATCCGCATGGCTATTCAAAATGCAACTGGTCCTAGAAGTGCTCTGTTTGTACCTGAA
















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|58672080|gb|CK060766.1|CK060766
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
EST: gi|58679026|gb|CK067713.1|CK067713
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
EST: gi|58658952|gb|CK047632.1|CK047632
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
EST: gi|58695675|gb|CK084362.1|CK084362
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
EST: gi|66928093|gb|CX114941.1|CX114941
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
EST: gi|29655723|gb|CB651998.1|CB651998
EST:     GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAG                         GATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA
genomic: GAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATA

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: 73 (upstream exon), 65 (downstream exon)
Score: 13

AATGGTGGAGGGAAAAAATGAGGACATATCAACAATTGAGCTTTGTGGTGGAGCAAGGATCCATTATATTTTTCAATCTATATATGTAAAAAGCTTAGAGgttcgtgatt ... ttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgttgtaccacatcattgttctataatgaagttatagaactttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG
                                           ctttttac  CT-rich tract
                         tataatgaagttata  TA-rich tract