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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgccgggtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatct...

Basic information

species Oryza sativa
transcript LOC_Os02g52140.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G862331_T04 (Zea mays), 5'ss of exon 2
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgccgggtgtgctcactgcctgcctaatttttactgatgcttt-tatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatct----
||||||||||||||| |||||||||| |||||||||||||||||||| || ||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||   |||||||||   |  |||    |||  ||||||||  ||  |||||   | || | |  | | |  | ||   ||    ||  | | |    
CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgttgtcttccta-tgtgctcac---ccaccttgccttt-ttgatgcttgataccttttttgcggtgtgtttaggtttcattattatggttcgatatgctatatac

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G108919_T03 (Zea mays), 5'ss of exon 2
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgccgggtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatct
|| |||||||| ||| |||||||||| | |||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||    || |||   |||  |||    ||| | |||||||                                                    
CTTCAGGAGCTTGACGAGATGAAGCGCAAGCTGAAGGAGATGGAGGaggaggccgccgccctccgcgatatgcaggccaaggtcgccaaggagatgcaaggttgtcttccta-cgtactc---gcccaccttgccttttc-gatgcttggt-------------------------------------------------

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G108919_T02 (Zea mays), 5'ss of exon 2
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgccgggtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatct----------
|| |||||||| ||| |||||||||| | |||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||| |||  ||    || |||   |||  |||    ||| | |||||||   ||||||     ||||  | || |  | |   |   |     |||||| |          
CTTCAGGAGCTTGACGAGATGAAGCGCAAGCTGAAGGAGATGGAGGAGGAGGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgttgtcttccta-cgtactc---gcccaccttgccttttc-gatgcttg-gtgttttc----ttgcagtgtgttgaggtttcactagagcggttcgatatgctataagcc

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S3_616V6.1 (Physcomitrella patens), 5'ss of exon 2
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccg---ccgggtgtgctcactgcctgcctaatttttactg-atgcttttatgtttttcttgttgcgatctgctatgttcatatcg--gcctcattcgatct----
         || ||  ||||||||  | |  ||||||||||||||||||||||||| || || || || ||||| || || || |  || ||||||   ||| |||       |  |   |  |||  ||  |  ||||  | |          ||   |||    ||   |  | | |  |  | |  |  ||  ||||  || |    
---------CTGGAGGAGATGAAGAAACGTTTGAAGGAGATGGAGGAAGAGGCCGCTGCTCTACGTGATATGCAAGCTAAAGTTGAGAAAGAGATGGGTGGTAGTCAAGgtttgaatcctcctactcgctctcgcatttcaattctgcatagcaattagtttggctttaaaacttaccaactctaaaaggatgctgcattt-atgtatca

upper sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 5'ss of exon 2
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccg---ccgggtgtgctcactgcctgcctaatttttactg---atgcttttatgtttttctt---gttgcgatctgctatgttcatatcggcctcattcgatct-
         || ||  ||||||||  | |  ||||||||||||| ||||| || || || || |||||||||||||| || ||||  |||||||||   ||| |||       |  | | || | |  ||  |  || || |||    |      || |  |   ||    |    |  || | | |   ||| |   | |    | |  
---------CTAGAGGAGATGAAGAAACGCTTGAAGGAGATGGAAGAAGAAGCTGCTGCTCTGCGCGACATGCAGGCTAAAGTCGAGAAGGAGATGGGCGGTAGTCAAGgtttgatttttcttatttactctcgcatgttaacttcgcacagcagtaagcctgattttgaatcagaaattgatttttctttat-gtttttacataaccga

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|32948090|gb|BP184662.1|BP184662
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|86830660|gb|CI293677.1|CI293677
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88326696|gb|CI658422.1|CI658422
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88376927|gb|CI639252.1|CI639252
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88353264|gb|CI654530.1|CI654530
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|66926559|gb|CX113407.1|CX113407
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88351377|gb|CI627393.1|CI627393
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|33664619|gb|CF295586.1|CF295586
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGTGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|218499461|gb|FG958244.1|FG958244
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88587501|gb|CI705252.1|CI705252
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCCAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|32948232|gb|BP184804.1|BP184804
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
EST: gi|88327844|gb|CI648241.1|CI648241
EST:     GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG                         GAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC
genomic: GGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgcc ... tgttttgtagGAGGAGATCCTAGCGCGTCTACAGCTGAGGCAAAGGAGCAGGTGGATGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAGgtggtccgccgggtgtgctcactgcctgcctaatttttactgatgcttttatgtttttcttgttgcgatctgctatgttcatatcggcctcattcgatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccggg