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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga...

Basic information

species Oryza sativa
transcript LOC_Os05g36110.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G073415_T03 (Zea mays), 5'ss of exon 4
-------TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga
       ||||||||||| ||| |||||||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||||||||                                                                                                          
GGTGGGTTCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTt----------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G048150_T03 (Zea mays), 5'ss of exon 4
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgat-----------tcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga
||||||||||| ||| |||||||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||| ||           ||||||| |  | ||| |||| ||||    |  | ||| | ||||  ||| ||||   ||   |||   | ||| |  | |  |           
TCAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTTCACCAGgtaatgtaattttttttcatacgcagctccaattctacgtgcaccaatgttgtccatccatattatctcttcaaaaaatattttagctttcctgtagagg-----------

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G073415_T01 (Zea mays), 5'ss of exon 4
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTT-CACCAGgtgat-----------tcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga
 |||||||||| ||| |||||||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||| |||||||||| |||||||| ||           ||||||| |  | ||| |||| ||||    |  | ||| | ||||  ||| ||||   ||   |||   | ||| |  | |  |           
-CAACTGTCTTCTGGGTTGGAGAATGGTTTATAAAAAAAATGCCATTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGTACTGCTGTTTTCACCAGgtaatgtaattttttttcatacgcagctccaattctacgtgcaccaatgttgtccatccatattatctcttcaaaaaatattttagctttcctgtagagg-----------

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 4
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgat-tcatacgtatata---caaatctatgtgctttgaaatagtctac--ccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga
||||| ||||| ||| |||||||||||||||| ||||||||||| ||||||||||||||||| |||||||| |||||||||||||||||||||||||||||| || | ||  ||| | |   | | |||| ||||     |||  |  ||  ||||  ||||||||   || | |||   | ||| |  | |  | | |       
TCAACGGTCTTCTGGGTTGGAGAATGGTTTATAAAGAAAATGCCCTTTGTAAGGCACATATACTCTGCATCAAAGCAAGTTAGCACTGCTGTTTCACCAGgtaatgtaattagtacacaactccattctacgtgcaccagaatgttgaacgtccatattatttcttcaaaatttattttagctttcctgtagaggagtcc------

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 4
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactc---attcatgtttttcacttg-gagtgacacattga
 | ||||| || ||||||||||||||||| || |||  ||||||  |||| ||||| ||||| |||||||| |||||  | ||  ||||  | || ||||||      ||| ||  | || |    |    || ||| |   | |   | ||  ||  |  |    ||   |||||| |   | |   |  ||  |||  | | 
GCCACTGTTTTCTGGATTGGAGAATGGTTCATAAAGCGAATGCCCCTTGTTAGGCATATATACTCTGCATCCAAGCAGATCAGTGCTGCAATATCTCCAGgtatgctctacataactgcata---gtccaattagaatttagccataaaagagtttgatggtgggttctgaattcatatggatgagcagtaagccacatgtag-

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 5'ss of exon 4
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgttt-ttcacttggagtgacacattga-----
|| || || || ||| |||| ||   |||||| | |  |||||| ||||| | |||||||||||| || || |||||| ||||||||||| |||| |||||| |  |     | | |||   |  || ||  || |     ||    | | |  ||| | |   |  ||   || |||  ||| || |  |       |       
TCTACAGTTTTCTGGCTTGGGGAGCAGTTTATAAGGCGAATGCCCTTTGTCAAGCACATATATTCAGCTTCTAAGCAAATTAGCACTGCTATTTCTCCAGgtaagac-----tgtgtactgtttcat-tgtcttcaccagttccctgctttagctttttctcgcatccaaatatatttgctcaattcgtctccttttcttcaaata

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|29621890|gb|CB626901.1|CB626901
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|29657648|gb|CB653923.1|CB653923
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|33795379|gb|CF323560.1|CF323560
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|27576459|gb|CA999153.1|CA999153
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|29657649|gb|CB653924.1|CB653924
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|29621889|gb|CB626900.1|CB626900
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|58687377|gb|CK076064.1|CK076064
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|88346159|gb|CI634032.1|CI634032
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|58695852|gb|CK084539.1|CK084539
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|86601840|gb|CI258516.1|CI258516
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|29621930|gb|CB626941.1|CB626941
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
EST: gi|29621929|gb|CB626940.1|CB626940
EST:     AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAG                         ATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA
genomic: AAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcata ... ttattgacagATCAAAATACAACGGCATTTAAAGAAGTTGCAATAATTAGTCATCCCCGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACTGTCTTTTGGATTGGAGAATGGTTTATTAAGAAAATGCCTTTTGTAAGGCACATATATTCTGCATCGAAGCAAGTTAGCACTGCTGTTTCACCAGgtgattcatacgtatatacaaatctatgtgctttgaaatagtctacccatgatatttctttttaactcattcatgtttttcacttggagtgacacattga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT