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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctgtatattactcttt...

Basic information

species Oryza sativa
transcript LOC_Os05g36110.2
intron # 3
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 3
lower sequence: GRMZM2G052855_T01 (Zea mays), 5'ss of exon 3
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctgtatattactcttt------
|| ||  ||||||| |||||||||||||| ||||||||| |  | ||||||||||| |||||||| ||||| |||||||| || || ||||| ||||| ||||| | ||      ||  ||   |   | || || |  ||   |||  | | ||||| | | ||  | |   ||        |   | | ||    |||      
TTGCCAATTGCTGTCACATTCTTCATCACTTGGTGGTTTATCCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTTGACATATTCGgtaattgttt-----atcttttattggtggtacttct-tttgccatgatacattactaaaatttagaattatcgatgccttttttcttttcttttctttttctatg

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G048150_T03 (Zea mays), 5'ss of exon 3
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaa-ataacagtctgtatattactcttt-------
|||||  ||||||| ||||||||| |||| ||||||||| || | ||||||||||| |||||||| ||||| |||||||| || || ||||| || || ||||| | ||      ||||||   |   | || || |  ||   |||  | | ||||| | |   | | |||  ||  | | | | |  || || |  |||       
TTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTTGACATGTTCGgtaattgttt-----atgctttatttgtggtacttct--ttgccatgatatattactaaaattgtagaattgtcaatgtcataattt-catttttccttttattttta

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G15360.2 (Glycine max), 5'ss of exon 3
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctgtatattactcttt-------
|| || ||||||||||| |||||||| || ||||||||| || ||||||||||||| || || |||||| | ||  | | ||| ||  | ||| | |||||| | |      ||  || ||  |  |  ||      |  | | ||    | ||  |      | | |  | | |||||    | | | ||||  |||         
TTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATAGATGTGTTTGgtgagt------aatttgttttgccttcaattaacacagctttgataattatattttccctcctcagaagttacaaatagggattt-tttattgttctactgtagat

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 3
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctgtatattactcttt------
|| || ||||||||||| |||||||| || ||||||||| || ||||||||||||| || || |||||| | ||  | | ||| ||  | ||| |||||||| | |  |  ||     |||   |    | |  | |  | |||||     | |      |   || |||| | |||||    | | | | ||  |||        
TTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATAGATGTATTTGgtgagtaatttaatttgcctttaattaacacagctttgataattat-----attttccctcctcaaaagtt-acaaatagggattttttttttgttctactgtata

upper sequence: LOC_Os05g36110.4 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctgg-atatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctg---tatattactcttt
|| ||||| |||||||||||| ||||||| ||||||||| |  |||| |||||||| || ||||||||  | || |  || |||||  |||| ||||||||||    |||   |||| |||||  || | ||  |  |  |   ||   |  || ||| |  ||||  |  |  |       |||||    ||| ||| |   |
TTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTTGACATATTTGgtatgaattg---aaattcttctgacttgtatcgtaatgttatgtactaagtaaaact-tgatgtagaaacttcgtctatgaagtctaagatatcttaatagat

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:     TATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|29657648|gb|CB653923.1|CB653923
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|13896941|gb|AU183277.1|AU183277
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTT
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTT
EST: gi|33795379|gb|CF323560.1|CF323560
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|27576459|gb|CA999153.1|CA999153
EST:     AGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: AGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|29657649|gb|CB653924.1|CB653924
EST:     TTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|29621889|gb|CB626900.1|CB626900
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|58695852|gb|CK084539.1|CK084539
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|29621930|gb|CB626941.1|CB626941
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGG-TTTTGACTTTCCTTGCTATTCATATTCCTAGTTGGAATATTT
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGAC-TTCCTTGCTATTCATATTCCTAGTTGGAATATTT
EST: gi|29621929|gb|CB626940.1|CB626940
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
EST: gi|87012610|gb|CI307358.1|CI307358
EST:     TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTG                         GCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG
genomic: TGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttg ... atcttttcagGCCTTGGGTTTTTGACTTCCTTGCTATTCATATTCCTAGTTGGAATATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTTGATATATTTGgtaactcttgcaaaaatgcttctctctggatatttgtacttattatggaaaaatactatactgtaatagttgagaaataacagtctgtatattactcttt

- - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG