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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattgcag

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacacctt-atttt----tgcatctgtattgcag
 | ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||||||||| | ||||||||||||||| ||||||||||  ||| |     || ||  ||  |  ||  | | | |     ||||||| | |||  | |||| |  |||||    ||  |    | |||||
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatt-tctttcatccattattgactgtacgtgtcattttaa-----agaaatcctctctattaacacttccattttctggtgtcttcaaactgcag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattgcag
 | |||||| | ||||| || || ||||| ||||| || |||||||||||||| ||||| |||||| | | |||| |||||||||| ||  |||||         |||      | |||  | ||    ||| || |||   | || ||  |  |   |  || |||   ||| || ||  |||
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtatggatacaaactta-----atctatctgtggttctgtcattcttg--agtc-tgcttcttactattttgttt---catttg-ataccag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgta---ttaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatca--tgtctgctgacaccttatttttgcatctgtattgcag---
 |||| ||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||| |    || ||||| ||||| ||  |||    || | |  ||  || || | |||  |  |     | || || | || ||| |  |     |  |    ||||  ||  ||||    || |    
CTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAGgttgacttgcttgtcttctggtcattgctgtacttttctgtcttgta-taaggaataaactaatgaccaatttattatactta-atctccggtgaaccag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctaca-----tatgaaaatgttatacttagaaatc---------atgtctgctgacaccttatttttg-catctgtattgcag
 | |||||| | ||||| || || || || || |||||||||||||||||||| ||||| |||||||| |  || || |||||||| ||  ||| | |  |     |  | | ||  || |      |  |||||  |   |  |||   |         || | || ||  |  |  |||||  ||| || |||||||
CTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAGgtgtgatttatgcttgatccataattatagtgatcaataaaatcctgggccaagatgccttcgcctgaatatttgatgtaatgtggtttttttcatgtg-attgcag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatt----tttgcatctgtattgcag-------------------------------------------------
|| || ||| ||||||| || || ||||| |||||||| |||||||||||||| ||||| ||||||   |  |||||||||||||||||  |||||  | ||  | |   | || ||   |  |     | || | |       || |  ||  |      | |||    || | |    | | |  |                                                 
TTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAGgtatgccttt--tttaaatttttgcagaaccttccttttttttcccccttcttctttccttttaggttgtcattaaggttggaagggatctggttgttgaaaccctttggaatgtgcaatactaatactgtttccatggtcccag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctc-------ttgttct-tagct---acatatgaaa-atgttatacttagaaatcatgtctgctg-------acaccttatttttg--catctgtattgcag----------------------------------------
 | |||||||| || ||||||||||| || || ||||| |||||||||||||||||||| |||||    | ||||||||||||||| ||  ||||||   ||  ||       | ||||  | | |   || |||| || |||  | | ||||||  |||   || |        ||   ||| ||| |  ||| | | |                                             
CTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAGgtattttgtttttcagccaaatagttcgatgggtggaacttatggaatatggcacatttagaatgcatcaatgttttgtttctacgatttactttaggacatttttgtgatgtcttgtaaagagattacaactgaactattcctttgtcacag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatttttg--catctgtattgcag------------------------------------------------------------
 | |||||||| ||||||||||| ||||| || || || |||||||||||| | ||||| |||||  | | ||| ||||||||||| ||  ||||   | ||||||     | ||  |    ||   |    |    | |  || |||||        | ||| | | |   ||| ||| ||                                                                
CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAGgtacgtcattgctcagccacatattttggcatcttataagtcctgtaatgaagcatgtgaatcaggaacttgtatctaaacatatgtcttcttagatttttgttagtactcttccaagtgtggtaccgaattgaattattcttctttgtcacag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctc----ttgttcttagctacat-----------atgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattgcag------------------------------------------
 | |||||||| |||||||||||||| || || ||||| ||||| ||||||||||||||||||||  | | ||| ||||||||||| ||  ||||||   || |||    |  || || |||| ||           | |||| |||   | |||  | |  | |  |   | || |  |  ||  || | |||                                               
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatc-tcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 11
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgt--attaccttgctc----ttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattg-cag-
 | |||||| | || |||| |||||||||||||||||| |||||||| || |||||||| ||||| || |  ||||| |||||||| ||| |||   |||| || |      ||  |   |||    |   | ||||   |  ||     | |  |  || ||    |     |||  |  |    |  || 
CTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAGgtttgttacatttcgaaaaattacttccagcatagttccagaatggggtcgttgctttttaaatgcgcagattagtgtcggttgtttaagcggaggtaga

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|58655643|gb|CK044323.1|CK044323
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCGAGGGA-GCGACCA
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGC-ACAGAAGCGACCA
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     GAGTGTTGTCTTAATGGGGATGGACTCCGTGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCA
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCA
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|29622204|gb|CB627215.1|CB627215
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
EST: gi|29644040|gb|CB649047.1|CB649047
EST:     GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG                         TAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC
genomic: GAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattacctt ... tgtattgcagTAATTTATTTCGGGTTTTTGGCTGTACTCCTGGGAGCACAGAAGCGACCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacaccttatttttgcatctgtattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA