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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCTGATGCCACCCACCCCAACCACCCCATCATGTACGCCAGCGCTGGCTTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcctcacacacacacacacataaacacatcaatccaattattcaattaataatcaattgtgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 1
TGTCTGATGCCACCCACCCCAACCACCCCATCATGTACGCCAGCGCTGGCTTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgt---tcgat--cctcacacacacacacacataaacacatcaat-ccaatt-attcaattaataatcaattgtgtgtgcag--------------------------------------
|||| |||||||||| |||  ||||||||||| | |||||||||||||| |||||||||||||| |||||  ||||||| ||||| ||||| ||||||||||   || ||    |||     | | |  | ||  |   || || |||||  | || | ||| | |  |     |  |||                                       
TGTCCGATGCCACCCGCCCTGACCACCCCATCCTCTACGCCAGCGCTGGATTCTTCAACATGACGGGCTACTCCTCCAATGAGGTCGTCGGAAGGAACTGgtgagtcaatggtttcaattcaatatattcctattctattccatgccaatcgaatcgaataacacttcaactaatacgcactgcacttacgcctcgctccgtctctcaactgcgtgcag

upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S509_6V6.1 (Physcomitrella patens), 5'ss of exon 3
TGTCTGATGCCACCCACCCCAACCACCCCATCATGTACGCCAGCGCTGGCTTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcc--tcacacacacacacacataa-acacatc---aatccaattattcaattaataatca------attgtgtgtgcag--------------------------------------------------------------
|||| ||||| || || ||| ||  ||||||| |||| || |||||||| |||||||| |||||||| || ||  ||||||||||| | ||  | ||||||| ||   |  |||||  | | ||      |  | |||      | |  | |  || || | ||| |      | |  ||| |||                                                               
TGTCGGATGCTACACAGCCCGACTTCCCCATCTTGTATGCAAGCGCTGGTTTCTTCAATATGACCGGGTACACACCCAAGGAGGTTATTGGACGAAACTGgtgcgtcacgatcacattcccccatgagcgatgcccattcttgcttctgtgaagcagtttacaattacaccctagttcgtgagcattactgagtagctgaggttttagagaatcattgcaaggcatgagtatgtgggcgtggattcag
















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|29627790|gb|CB632801.1|CB632801
EST:     TTCTTCAACATGACCGGCTACACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTC
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTC
EST: gi|29622370|gb|CB627381.1|CB627381
EST:     TTCTTCAACATGACCGGCTACACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29644411|gb|CB649418.1|CB649418
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29624447|gb|CB629458.1|CB629458
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAG
EST: gi|29681858|gb|CB678133.1|CB678133
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29668387|gb|CB664662.1|CB664662
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29662103|gb|CB658378.1|CB658378
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29668422|gb|CB664697.1|CB664697
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29624476|gb|CB629487.1|CB629487
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29621737|gb|CB626748.1|CB626748
EST:     TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
EST: gi|29623832|gb|CB628843.1|CB628843
EST:     TTCTTCAACATGACCGGCTACACCTCCAAGGAGGTTGTCGGCAGGAACTG                         CCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG
genomic: TTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAG

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: 63 (upstream exon), 67 (downstream exon)
Score: 11

TGTCTGATGCCACCCACCCCAACCACCCCATCATGTACGCCAGCGCTGGCTTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcct ... gtgtgtgcagCCGCTTCCTTCAAGGCTCTGGCACCGACCCCCATGAGATTGACAAGATCAGGCAATCCCTCGCAAATGGCTCCAACTATTGTGGCCGCATCCTCAACTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCTGATGCCACCCACCCCAACCACCCCATCATGTACGCCAGCGCTGGCTTCTTCAACATGACCGGCTATACCTCCAAGGAGGTTGTCGGCAGGAACTGgttcgatcctcacacacacacacacataaacacatcaatccaattattcaattaataatcaattgtgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG