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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagagaatgtttaaaaggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatcaactat...

Basic information

species Oryza sativa
transcript LOC_Os06g30460.3
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G082664_T01 (Zea mays), 5'ss of exon 15
GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagagaatgtttaaaaggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatca-actat---
||||||||||| || || ||||| ||||| ||||||||||||||||| ||||||||| ||||||||  |   ||||||   || |||||       |||  |   | |  |  | |     ||     |||    |  || | |||  ||||    |   | ||   
GGCCTGATGACCCCAATAATAAGGAATGCGGATCAAAAGACTATATCTGCAATATCCGCAGAGgtacaat--aatgttgtcaaagttcagagcagatgtt-tgcgtgctaagatgcccagacagtttttgtttttga-acttctaattcttgactccttgccatcaa

upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA20G33080.1 (Glycine max), 5'ss of exon 18
GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgta-tgagagaatgtttaaa-aggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatcaactat-
||| |||||||||| || |||| |||||| ||||| ||||| ||||| || || |||||||||||| |   |     |||    |||||     ||| || | |  |   ||||  |       |    |||  |    |   |   |     |  | |||   | 
GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttgtgtaggtttctggttaatgactttatgatagaaactggaatataccgtatgctattaac---taagaaatcagggagcaaagctc

upper sequence: LOC_Os06g30460.4 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA10G34480.1 (Glycine max), 5'ss of exon 14
GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgta-tgagagaatgtttaaa-aggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatcaactat
||| |||||||||| || |||| |||||| ||||| ||||| ||||| || || |||||||||||| |   |     ||||   |||||     ||| || | |  |   ||||  |         ||||| |  |   | |   ||||    | |||||     
GGCTTGATGACTCCAATAATAAAAAATGCTGATCAGAAGACAATATCTGCTATCTCCTCAGAGgtaattttatctcatttatgtaggtttctggttagtgactttatgatagaaact---------gaaatataccgaacgctattaac-tgagaaatcag----

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|58692196|gb|CK080883.1|CK080883
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
EST: gi|27578288|gb|CB000983.1|CB000983
EST:     TATTATAAGAAATGCAGAATCAAA-GACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAAGCACGTGCTGGG
genomic: TATTATAAGAAATGCAGA-TCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGG
EST: gi|88849307|gb|CI087829.1|CI087829
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
EST: gi|218482631|gb|FG947596.1|FG947596
EST:     CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAG                         GTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA
genomic: CTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagaga ... atcactgtagGTTAAGCAGTTGGCTGAAAAGGCACGTGCTGGGAAGCTTGCTCCTAATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTGATGACTCCTATTATAAGAAATGCAGATCAAAAGACTATATCAGCAATATCCTCAGAGgtatgagagaatgtttaaaaggttcaaccttactgtcatagtttcagaagttctttagcatgaaatgtcacaggcacatgtaacgcttgtaatcaactat

- - - - - - - - - - AAGAAA
- - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - -  AGATCA