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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt...

Basic information

species Oryza sativa
transcript LOC_Os04g40310.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgt---tgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt
|||| |||  |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||||     | | |||  ||  |   |||  | |   |   | || ||  ||    |     |      || | | |  || |     | | |     |    
GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacggagtgtcggttggggtcggctgcgtttcatgtttattatgatttttccgatatgttatactccctccttttatataagtatatgacaccgtt---

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt--------
 ||| |  |||| |||||||||||||||||||||||||||||||| |||||||| || ||||| ||||||||||| |||||||| ||||| |||||||||||||    || || ||  | |||    ||||   ||   | |   |  | |  |  ||||    |   ||     ||| || |     ||||   |            
CCACGACAACGTTGACATCGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAGgtac---tcactcacgt-tcacggtttctttctgctcaagctaaataatagcagctgaataattag--gttttatgatcttaata--aaatgaaattaagagaatgaa

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt---
 ||  |  | || || || || |||||||||||||||||||| || |||||||| || ||||| ||||||||||| |||||||| || || ||||| |||||  |  |    ||| | |  |||     |  | || ||    | |   |  | |  ||  |  ||  ||  |   | |   | |   |||   || |||   
CCATGATAATGTTGATATTGTTGTCATCAGGGAGAACACCGAAGGCGAGTACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgtgctctt-cctctcctctcgc-tttctcacactttttacatatagggtcttgctaagggt-actagttaacgaactaaaaagagaaatcatttactttga

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctg-ttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt-------
 ||  |  | || || ||||| |||||||||||||||||||| || || ||||| || ||||| ||||||||||| |||||||| || || ||||| ||||| ||      |||  |    | | ||||||     | || || | | ||      | | | |    |  ||  |   | ||      | || ||||  |        
CCATGATAATGTGGATATCGTTGTCATCAGGGAGAACACCGAAGGCGAATACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgt-----tcttccactcccctcgctttctcacgctttttatatattatc---aaatttgttttctatgtttttctattatttatttatttgtttttgaaattag

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacggg--ccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttg-acgtctaatgtgttcctt----------------------
 ||  || | || |||||||| |||||||| |||||||| || || |||||| ||||||| ||||||||||| || || || ||||| ||||| || |||||  |    || || ||   ||   | || ||||     |   | ||| || || | |  |||  |    |    | |  |||| | ||    |||| |  ||                      
CCATGAGAATGTTGACATCGTTGTCATCAGAGAGAACACTGAAGGTGAGTACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattccgatttc---tgctcctcgttttggat--tcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttag

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctt-tgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt-
|||| | || || || || || ||  | ||||||||||| ||||| |||||| | ||||| |||||||||||||| |||||||| ||||| ||||| ||||||  | |   |     |    | |  ||  ||     |    |    | |  |   |  |  |       | |   |     |  |  |||| |  || | 
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaacgtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggtt--ctgttttggtaagaaaaaaaatataaaatgcgaccccta

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaat------ctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt
||||||| | || || || ||||| ||  ||||||| || || || ||||||||||||||||||||||||||||| ||||| ||||| || ||||| |||||   |     |      || |  ||| |     ||||  | |||      || || |        |    | ||    | ||  | || |   | |  ||     
GCACCAGAATGTGGATATAGTCGTGATTCGGGAGAATACGGAAGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgatttgttattaccttgtctgatggttattttgg-ccgtttcccaatgctgttcaattttccttttctcgattttagaggtagaggatcatttggt-----

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt-----
 ||| |  | ||| ||||||| || ||  |||||||||| |||||||||||||| || || || ||||||||||| || || ||||| |||||||| || ||||    |    || | || |    |  ||| | ||  ||| | | ||  ||     ||    |    |   |  |  | |||   | |||  |   |      
CCACGACAATGTCAACATCGTGGTAATTCGGGAGAACACAGAGGGGGAGTACTCTGGTCTTGAACACGAGGTCGTCCCTGGGGTCGTGGAGAGCCTGAAAgtacctatctcattcacctg-cttttgaattgatatga-gttatttatttatttatttat--ttatttatttgtaaacatggacaa-tgatgcatctgtgaatcg

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaa----tctcgcgtgacgcgcg-ctttgctctgttgttgtgtgt--tggttggagaatcgcc-acccgtgcatcgattttgacgtctaatgtgttcctt
 ||  |  | ||| |||| || || ||  ||||||| ||||| |||||||| || || || |||||||||||||| ||||| |||||||||||||| |||||||           |||  | |||       |  | |||| | ||||||  |  || ||| |  ||   |   ||  ||||   |||| ||| ||  ||| |     
CCATGACAATGTCAACATTGTGGTTATTCGGGAGAATACCGAAGGGGAGTATTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTCGTCGAGAGCCTTAAGgtacatatttcgttttctgacctgaaaaataacactactctat-gttgtgcctagtgattgtaatattttctgtccaagcattt-ttttcacgcctt-tgttt-----

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcc--aatctcgcgtgacgcgcgctttgctctgtt-gttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt
 ||| |  | ||| |||| || || ||  | |||||||| || || |||||||| || || |||||||||||||| ||||| || ||||||||||||||||||     |  | ||| |       |  |   | | |  ||   || || |    ||  |   |    |   |  |   |||| |   |  | | |  | | |
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcgg---caaatcttctttactcatttcgttatgcacttttctgcat

upper sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 1
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggccaatctcgcgtgacgcgcgctttgctctgttgttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt
 ||  |  ||||| |||| || || ||| ||||||||||||||||||||||| | || || |||||||||||||| || || || ||||||   ||||||||||   ||||| ||   |  |    ||||||||| |  | |     |  |||         |  |  | ||| |                         
CCATGACAACGTCAACATTGTTGTGATCCGGGAGAACACCGAGGGGGAGTACGCCGGCCTGGAGCACGAGGTCGTCCCGGGTGTTGTCGAGTCTCTCAAGgtac--tccaatttcttct--cctctgctttgctcggccgctccagctacgttt--------cttcttgcgcaccag-----------------------

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|29687051|gb|CB683326.1|CB683326
EST:     ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAG-C-C---                         ----T--C-AAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcca ... cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
EST: gi|29662276|gb|CB658551.1|CB658551
EST:     ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAG                         GTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcca ... cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT