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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaactgggtttgtttgctgctctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaact--gggtttgtttgctgctctg-cag
|||||||||| ||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||| | ||||||   ||   |        |||  ||  || |||||||  || || || ||   |||||| ||||||    |  |||
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagta-gagagggattgtgcagcattg----tttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcag

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagta-tgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgtt-gctaactgggtttgtttgctgctctg-cag------------
| || ||  |   ||| ||||| || || || ||||||||||| || ||||| || ||||||||||| ||||| ||||||||| | || || || |||||||| |||  |    |   |  || |   |   | || ||     || ||   ||  | |  | | | ||  |||||||   |   || | |            
AACGATATTTATCTGGGTTTACTAAAGTCGACGACAACCGCTATTCCATGAAAATCTTCTTTGAGATTCGCAAGCAGAAGTATTTGGAAGCTCTGGATAAgtatgtagcgatttgtgccgcgtgcgggctc-atttctaccacttgaagcaaaacacatcagatgaatg--tttgtttagaggaatggctgtgtcttggtttc

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacat--------gtccctacaggaattttaggtg--ctggagtggaaagcgttgctaactgggtttgtttgctgctctg--cag
| || ||  |   ||| || || ||||| |||||||||||||| || ||||| || ||||||||||| || ||||| ||||| || || || || || ||||| ||||      | |  |        |||  |   |  ||| |  |    ||  | ||      ||  |   |||||      || |    ||   ||
AACGATATTTATCTGGGTTCACTAAGGTGGATGACAACCGCTATTCAATGAAAATCTTCTTTGAGATACGGAAACAAAAGTACCTGGAAGCTCTGGACAAgtacgtattcagttgcatctcgtttggagtcattggggtgattcttagcagactacattgatttaagtctcgttctgggggaagatgttatcttggttag

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ17248 (Selaginella moellendorffii), 5'ss of exon 2
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctgg-agtggaaagcgttgctaactgggtttgtttgctgctctgcag
|||| ||| |    |||||||||||||| |||||||| ||||| || |||||||| || || || || ||||| || |||||| | || || || || |||||||       | |    | | |          |||    ||||| ||   |  |  ||| || ||   | ||    | |        
AGCGTTACTTGTCGGGCTTTACCAAGGTAGATGACAATCGCTATTCAATGAAGATCTTTTTCGAAATTCGCAAGCAAAAGTATTTGGAAGCACTGGACAAgtaag-------gagtttgtttgctattgattcgtttcttcgctggtagctaacgggtttgttacctctctctggcgtcag--------

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ30926 (Selaginella moellendorffii), 5'ss of exon 2
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaactgggtttgtttgctgctctgcag
|||| ||| |    |||||||||||||| |||||||| ||||| || |||||||| || || || || ||||| || |||||| | || || || || |||||||     |||      ||    |       || |    ||||   |  || | |||  | ||    | | | ||  | || |   
AGCGTTACTTGTCGGGCTTTACCAAGGTAGATGACAATCGCTATTCAATGAAGATCTTTTTCGAAATTCGCAAGCAAAAGTATTTGGAAGCACTGGACAAgtaag-----gagtttgtttggtattgattcgtttctt--cgctgatatctaacgggtttgttacctc-tctctctggcg-tcag---

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|29656775|gb|CB653050.1|CB653050
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|29629469|gb|CB634478.1|CB634478
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|27334445|gb|CA882896.1|CA882896
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|88724837|gb|CI748096.1|CI748096
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGG
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGG
EST: gi|88298806|gb|CI566003.1|CI566003
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|58662919|gb|CK051605.1|CK051605
EST:     AAGATATTCTTTTCGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|88412321|gb|CI573597.1|CI573597
EST:     ACATATTCTTTGAGATCCGCAAACAGAAGCTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCG
genomic: AGATATTCTTTGAGATCCGCAAACAGAAG-TATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCG
EST: gi|58652923|gb|CK041603.1|CK041603
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|88426720|gb|CI584083.1|CI584083
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|29656774|gb|CB653049.1|CB653049
EST:     AACAGAAGTATCTTGAGGGCCTTGATAA                         GNATGATCGCCCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
EST: gi|88717854|gb|CI739366.1|CI739366
EST:     AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAA                         GCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgg ... tgctctgcagGCATGATCGTTCGAAGGCGGTTGAAATCTTGGTCAAGGACCTGAAGGTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaactgggtttgtttgctgctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT