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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaattcttaactcagtaattgattccttatttgtgtaattttcttcag

Basic information

species Oryza sativa
transcript LOC_Os01g34620.6
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.5 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 6
CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaattcttaactcagtaattgattccttatttgtgtaattttcttcag
 |||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||    |||| |||||||||       || |  |  ||||   || |      |||     || | |||| | |        |||   ||||| |||  |    |||| | ||||||
TAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGGTCTGACATCATATTAAGCTTGCACCAGgcaagt-------ttctgacttgtttcgttagc-----atattagcttattgtctttact--------agtggctgatttctt--tgtcataatctccttcag

upper sequence: LOC_Os01g34620.5 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 5'ss of exon 6
CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagcttattg-tccccggttttcataaccatgtgtatccatctactttcttaattcttaactcagtaattgattccttatttgtgtaattttcttcag
| ||||||| ||||||||||||||||| || || || |||||  | |||||||||||||| ||  |  | ||||| ||||  | |     |||   |  | | || |  |   ||  || |   || || |    |||  ||    || ||  |   |                         
CCACTGGCCCACATTTCCACAAATATTCATAAAGGGGGAGTTCATAGGGGGATCTGATATTATTCTCAACATGCACCAGgttaatttctatatcaatatctgtttcttgttttca-atgcagtaatatattgctctaacactgtggtctgtcctgtgtag-----------------------
















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|33688088|gb|CF316327.1|CF316327
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
EST: gi|86501844|gb|CI144477.1|CI144477
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
EST: gi|86510934|gb|CI153567.1|CI153567
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
EST: gi|33662135|gb|CF293102.1|CF293102
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
EST: gi|86825099|gb|CI358251.1|CI358251
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAAC-A
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     TCAAAGGAGAGTAAGTAGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTACGGATGTGCTTGG
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGG
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
EST: gi|86431345|gb|CI084956.1|CI084956
EST:     TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAG                         AAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA
genomic: TCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagc ... ttttcttcagAAGGGTCAGCTTAAGGATGTGCTTGGTGATATTGCACAAAAGCGTGAACAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACTGGCCTACATTTCCACAAATATTTATCAAAGGAGAGTTTGTTGGGGGATCTGATATCATATTAGATATGCATCAGgcaagtgagcttattgtccccggttttcataaccatgtgtatccatctactttcttaattcttaactcagtaattgattccttatttgtgtaattttcttcag

- - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - -  AGGAGA