Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcatctattgctcaaacaatatgtttagcttttgtaactaactcttagtagaactagtgccaaattgccaaaaaacttgccagatgttaatgtggtgcacaattgatacaccag

Basic information

species Oryza sativa
transcript LOC_Os03g06620.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G165998_T03 (Zea mays), 5'ss of exon 2
GAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcatctattgctcaaacaatatgtttagcttttgtaactaactcttagtagaactagtgccaaattgccaaaaaacttgccagatgttaatgtggtgcacaattgatacaccag
||||||||| |||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||   ||||||||| ||||||| |||    ||||| |      |  | |||   | | ||    || ||    ||||  |||  |||   | |  | | |    ||  |  |                        
GAGGTCATCCAAGCATGGTACATGGACGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTCGACAAACTTTCCGgtttgtacatgccctgctctag-----tcctgagcccatatgacatcttcatatactaactgatgctgaatg--ctactaccatcatggacatccag-----------------------

upper sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G14716.1 (Arabidopsis thaliana), 5'ss of exon 2
GAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcatctat-tgctcaaa--caatatgtttagcttt-tgtaactaactcttagtagaactagtgccaaattgccaaaaaacttgccagatgttaatgtggtgcacaattgatacaccag
|| || ||  |||||||||| |||||||| ||||||||||| ||||| |||||||| ||    || || ||||| ||  |  |  |   ||||||| |||||       | | | || |  ||  |||| |  ||  || |   |  |||  |  |   | |  || ||      |||                                              
GAAGTGATTCAAGCTTGGTATATGGATGATAGTGAAGAGGATCAGAGACTTCCTCACCACAAGGATCCTAAAGAGTTTGTATCGTTGGACAAACTTGCAGgtccccctctttgtgtgtttcaattcaatgttgttctctctgcttctctattttgtttcacatgtaatgtttgtgtgcag--------------------------------------------
















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|33664076|gb|CF295043.1|CF295043
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88410806|gb|CI578612.1|CI578612
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88432267|gb|CI565300.1|CI565300
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88392897|gb|CI614779.1|CI614779
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|700773|gb|D47064.1|D47064
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|58591300|gb|CF989608.1|CF989608
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88300984|gb|CI592164.1|CI592164
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|313084041|gb|HO213824.1|HO213824
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|218497580|gb|FG955135.1|FG955135
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88573345|gb|CI664916.1|CI664916
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|58657720|gb|CK046400.1|CK046400
EST:     TGAGCCCAAAG-ATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|33662546|gb|CF293513.1|CF293513
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|117246064|gb|CT862529.1|CT862529
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|66916156|gb|CX103004.1|CX103004
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88738682|gb|CI762190.1|CI762190
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88423723|gb|CI617075.1|CI617075
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88341716|gb|CI641468.1|CI641468
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88311755|gb|CI574972.1|CI574972
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88728915|gb|CI752425.1|CI752425
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88354257|gb|CI637823.1|CI637823
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88398782|gb|CI601118.1|CI601118
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88354747|gb|CI614025.1|CI614025
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88337236|gb|CI629526.1|CI629526
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88719684|gb|CI743194.1|CI743194
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88447697|gb|CI579773.1|CI579773
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|33659100|gb|CF281713.1|CF281713
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88570475|gb|CI661848.1|CI661848
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88371298|gb|CI600146.1|CI600146
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88693640|gb|CI737215.1|CI737215
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|218494503|gb|FG957959.1|FG957959
EST:     TAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88445319|gb|CI587213.1|CI587213
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88575234|gb|CI669379.1|CI669379
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
EST: gi|88669169|gb|CI720126.1|CI720126
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCCGCCTGAATGCTGATGACTGGGAGAATGAT
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGC-GCCTGAATGCTGATGACTGGGAGAATGAT
EST: gi|569576|gb|D40425.1|D40425
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTTGGGAGAATGAT
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACT-GGGAGAATGAT
EST: gi|88730508|gb|CI754121.1|CI754121
EST:     TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAG                         AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG
genomic: TCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 74 (downstream exon)
Score: 215

GAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcat ... gatacaccagAGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTCATCGAAGCTTGGTACATGGATGACAGTGAAGAGGACCAGAGGCTTCCTCATCATCGTGAGCCCAAAGAATTCATTCCTCTTAGCAAACTTTCAGgtttgtgcatctattgctcaaacaatatgtttagcttttgtaactaactcttagtagaactagtgccaaattgccaaaaaacttgccagatgttaatgtggtgcacaattgatacaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA