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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_Os01g69130.1
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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgttgtaccacatcattgttctataatgaagttatagaactttttacacagGATGTTGACCCTTGTGAAGATGTTACCGATGAAGACATCCGTATGGCTATACAGAACGCAACTGGTCCTAGGAGTGCTTTGTTCGTACCTGAG
                                           ctttttac  CT-rich tract
                         tataatgaagttata  TA-rich tract