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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttcttacttctatttactcactaactaatcattatcactgcttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat...

Basic information

species Oryza sativa
transcript LOC_Os11g39220.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G419782_T01 (Zea mays), 5'ss of exon 2
----------------ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcattatcactg-cttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat
                 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||     || ||   ||  ||| |   ||| || |                              
TCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGgttgttttgcaatgacagaactacatcatggttaggttctccacttatatttatttattatccaataattggtgttgtctctattattttgc---ttagcact------------------------------

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G419782_T02 (Zea mays), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcatta------tcactgcttggttgctttacactttatcagtccaaacctcctagttcaac--ctccatcccat-----------------------------------------------------------------------------------
 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||       || ||  |   ||||||  |||||||||| |  | |  |||   | |||   ||| || |  |                                                                                   
GTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGTTGTTTTGCAATGACAGAACTACATCATGgttaggttctccacttatatttatttattatccaataattggtgttgtctctattattttgcttagcactttatcaatgtacag-tccagctacaatgtctcaatactgttgtgttctgtttattttgaatggcgcacagtagggcttgtacccagcacctaacgcactgttgtgttcttttcttgcaaatag

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G445791_T02 (Zea mays), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcattatcactgcttgg------ttgctttacactttatcagtccaaacctcctagttcaac--ctccatcccat-----------------------------------------------------------------------------------
 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||    |||  |        ||||||  |||||||||| |  | |  |||   | ||    ||| || |  |                                                                                   
GTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGTTGTTTTGCAATGACAGAACTACATCATGgttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgcttagcactttatcaatgtacag-tccagctacagtgtctcaatactgttgtgttctgtttattttgaatggcgcacagtagggcttgtacccagcacctaacgcactgttgtgttcttttcttgcaaatag

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G820287_T02 (Zea mays), 5'ss of exon 2
----------------ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcattatcactg-cttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat
                 | |||||||| |||||||||||||||||||||| ||      | ||||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||    ||| ||   ||  ||| |   ||| || |                              
TCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGT------ATGGAATTGACAATTTGGATTATCCAGgttgttttgcaatgacagaactacatcatggttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgc---ttagcact------------------------------

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G099666_T01 (Zea mays), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcattatcactgcttgg------ttgctttacactttatcagtccaaacctcctagttcaac--ctccatcccat-----------------------------------------------------------------------------------
 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| |||||||| || |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||    |||  |        ||||||  || ||||||| |  | |  | |   | ||    ||| || |  |                                                                                   
GTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGCTGTTTCGCAATGACAGAACTACATCATGgttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgcttagcaatttatcaatgtacag-tgcagctacagtgtctcaatactgttgtgttctgtttattttgaatggcacacagtagggcttgtacccagcacctaacgcactgttgtgttcttttctcgcaaatag

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G445791_T01 (Zea mays), 5'ss of exon 2
----------------ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcattatcactg-cttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat
                 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| || |||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||    ||| ||   ||  ||| |   ||| || |                              
TCTCTGGGGTGGTTCTGTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGgttgttttgcaatgacagaactacatcatggttaggttctccacttatatttatttattatccaataattggtgctgtctctattattttgc---ttagcact------------------------------

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G045376_T01 (Zea mays), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt--acttctatttactcactaactaatcatt------atcactgcttggttgctttacactttatcagtccaaacctcctagttcaac--ctccatcccat-----------------------------------------------------------------------------------
 | |||||||| |||||||||||||||||||||| || |||||| ||||| ||||||||||||||||| ||||||||||| |||||||| || || ||||||||| |  |  |||| |||||| | | || | ||| |||      ||| ||  |   ||||||  |||||||||| |  | |  |||   | ||    ||| || |  |                                                                                   
GTCATAAATCTAGGAACCAAAAAGCACAGAGATAAGTACTTTGATGGAATTGACAATTTGGATTATCCAGGCTGTTTTGCAATGACAGAACTACATCATGgttaggttctccacttatatttatttattatccaataattggtgctatctctattattttgcttagcactttatcaatgtacag-tccagctacagtgtctcaatactgttgtgttctgtttattttgaatggcgcacagtagggcttgtacccagcacctaacgcaatgttgtgttcttttcttgcaaatag

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA05G31390.1 (Glycine max), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttcttacttctatttactcactaactaatcattat-cactgcttggttgctttacacttta---tcagtccaaacctcctagttcaacctccatcccat
 |  | ||| |||| ||||| ||||| |  |||| || |||||| || || || || ||||| || ||||| |||||||||||||| ||||| |||||||||    | | |  ||| | | ||  |||||  | |||  | | |  ||||    ||||    |||    ||| |      ||  | ||| |   ||  |  | |
GTTCTCAATTTGGGGACCAAGAAGCATAAGGATAAGTACTTTGATGGGATTGATAACTTGGACTACCCTGGTTGTTTTGCTATGACCGAGCTTCACCATGgt--actttcatctctttcttctt-ctaacataacatgttgctcaacttgtaaactttgttttttcatctcattgttggactgttggtt-agtgtcactgactt

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 2
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttc--ttacttctattta---ctcactaactaatcattatcactgcttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat
 |  | ||  | ||||| ||||| || |  |||| || || ||| |  || ||||||||||| ||||| |||||||||||||||||||| ||||| ||||||  ||||   | ||  |||  |   ||   |   |  | | | |    | ||   || || |   |||    ||  || | |   |  || |    |||     
GTGCTCAACTTAGGAACTAAAAAACATAAGGATAAGTACTATGATGTTATTGACAATTTGGAGTATCCAGGCTGTTTTGCTATGACAGAACTGCATCATGgtaggttcatctgctggtatccaggactttttgtttgttgacttttcaggattcagtgtttcattattttgtggttgaagcatatca--tctataggcatgg---

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|29641782|gb|CB646789.1|CB646789
EST:     GAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: GAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|29678643|gb|CB674918.1|CB674918
EST:     CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|58610022|gb|CK038055.1|CK038055
EST:     CGACAATTTGGATGATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAGACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
EST: gi|29678050|gb|CB674325.1|CB674325
EST:     CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATG                         GATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG
genomic: CGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttctt ... ttcttaacagGATCTAATGTCCAGGCCCTACAAACTACTGCTACATTCGATCCAGTTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATAAATCTGGGAACCAAAAAGCACAGAGATAGGTTCTTTGACGGAATCGACAATTTGGATTATCCTGGCTGTTTTGCTATGACAGAGCTGCACCATGgttagttcttacttctatttactcactaactaatcattatcactgcttggttgctttacactttatcagtccaaacctcctagttcaacctccatcccat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC