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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCCACTTAATGAGAAATTTGATCCAAATAAGCATGCTGCGCTTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctcttccgataattttggtatagggtttttaccccctttctcttctgaaataagagctcattcaagtccggtacttaacctcaatgtttgttggt...

Basic information

species Oryza sativa
transcript LOC_Os08g25090.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25090.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G002440_T01 (Zea mays), 5'ss of exon 4
TGATCCACTTAATGAGAAATTTGATCCAAATAAGCATGCTGCGCTTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctcttccgataattttggtatagggtttttacccc-ctttctcttctgaaataagagctcattcaagtccggtacttaacctcaatgtttgttggt--
||||||  | |||||||| ||||||||||||| |||   |||  ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||  |||   ||||  |  | |  | ||  || |   | |   | | ||    ||  |  | | |||||  | |   | |      ||    |||    
TGATCCTTTGAATGAGAAGTTTGATCCAAATAGGCACTATGCCATTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCTGCTGTTGTGAAGgtatgcatttct--taatgctactttttgtttactagcaaacatggccatgtgttgcaatggaacttacaagtt-gttgtgtgattcttgtgccaattgaact
















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|86594295|gb|CI251167.1|CI251167
EST:     GGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: GGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88548809|gb|CI478638.1|CI478638
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88992829|gb|CI035791.1|CI035791
EST:     TCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: TCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88508434|gb|CI435940.1|CI435940
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88503823|gb|CI431329.1|CI431329
EST:     AAATTCCTGATCCTTCNAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCTTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88216044|gb|CI215893.1|CI215893
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88515130|gb|CI442784.1|CI442784
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|1632330|gb|C20059.1|C20059
EST:     AAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88541182|gb|CI468436.1|CI468436
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88549135|gb|CI478995.1|CI478995
EST:     AANTTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|29665018|gb|CB661293.1|CB661293
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|27554120|gb|CA998020.1|CA998020
EST:     AAATTCCTGATCCTTCAAAACCATCANGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|163928223|gb|EG714627.1|EG714627
EST:     CATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: CATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|218505197|gb|FG965305.1|FG965305
EST:     CGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
genomic: CGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC
EST: gi|88526319|gb|CI452450.1|CI452450
EST:     AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAG                         GTGGGCTACATGCTACATGATCGTGTTCTCCTTCCTGCGGAAGTTGGTGTC
genomic: AAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctctt ... tcttttttagGTGGGCTACATGCTACATGATCGTGTTCTCCGTCCTGCGGAAGTTGGTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCCACTTAATGAGAAATTTGATCCAAATAAGCATGCTGCGCTTTTCCAAATTCCTGATCCTTCAAAACCATCAGGAACTGTTGCGGCTGTTGTGAAGgtatgctcttccgataattttggtatagggtttttaccccctttctcttctgaaataagagctcattcaagtccggtacttaacctcaatgtttgttggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT