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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g17180.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag
||| ||||||||||| || |||||||||||||| |||||   |||||||||||||||||||||||||||||||||||| |||||||| || || ||||||||    ||| |||  ||||  ||  |    ||| |||| |  ||    ||||||||||| | | ||||  ||  | | ||||
CATAATGGATTTTGTTTCTGGATCAGCTAGTCAGAACTTTAGTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcagatttgttggtttatgtaagatttt-tttaatgtgctgaa---ctgttctttatagcct-ctatcattcaccgtgcag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag
||| ||||||||||| || |||||||||||||| || ||  ||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||||    ||| |||| |||    |   | || || | ||    || |   ||||||||||||||  | || ||||||| ||||
CATAATGGATTTTGTTTCTGGATCAGCTAGTCAGAATTTTACTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCGCTTGAAGAAGCGAAAAATGAGgtcggatttgttgcattagatgagaaaaaaatt-aagtgttgaacg---gttctttatacctt-tttttatttgctgtgcag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgtt--cagtttcttgccttatcca-aattagaattttatgtaccaaaagattgttctttataccttgc-tattctttgctgcgcag
||||||||| | |||||| || |||||||| || |||||    |||||||| || ||||| |||||||| |||||||| |||||||| |||||||||||||||   |  ||  | | |||||      |     |   |||   ||   | | || | | ||  ||   | |   |   |   |||
CATTATGGACTATGTCTCAGGTTCAGCTAGCCAGAACTTTGGCCTTCTGCAGGAATTCTATCAGACAACTCTGAAAGCCCTTGAAGAAGCAAAGAATGAGgttaatacatttatacattatctttggctcatggtaattgtcataattcaatcttatgtttattttttatgtcactcattttacag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgtt----cagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgc-tattctttgctgcgcag
||||||||| | |||||| || ||||||||||| |||||    |||||||| || ||||| |||||||||||| |||| |||||||| |||||||||||||||    || ||   |    | |     | |   | ||    |  || | | | || | | ||  ||   | |   |   |   |||
CATTATGGACTATGTCTCTGGTTCAGCTAGTCAGAACTTTGGCCTTCTGCAGGAATTCTATCAGACAACACTGCAAGCCCTTGAAGAAGCAAAGAATGAGgttaatacatttagatattatctttggctcatggtatttgtcattaatacaatcttatgtttattttttatgtcactcattttacag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcag-------tttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag
 || |||||||| ||||| ||||| ||||| || |||      || |||||||||||||| ||||| ||  ||||||| ||||||||||| |||||||||||| ||       |   | |  || |  ||  ||    ||  | |  |||  | ||| | ||   | | |    || |||  | | |||
TATCATGGATTTCGTCTCTGGATCTGCTAGCCAGAACACTGGCCTGCTGCAAGAGTTCTATCAGACCACTTTGAAAGCCCTTGAAGAGGCTAAGAATGAGgtttagaagctattcattcgttttgtataagctactgattcct-tctcaatcgtttggtgttgtgaacatat--ttttttctttcacag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcag----tttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattct-ttgctgcgcag
||| ||||||||||| || ||||||||||| || || ||    |||||||||||||| |||||||| || ||||| || |||||||||||||| |||||||||  |    ||| ||| ||||  |    | |   || |  |    |     |    |||| |   |  || ||| ||| || ||||
CATCATGGATTTTGTTTCTGGATCAGCTAGCCAGAATTTTGGGCTTCTGCAAGAGTTTTACCAGACCACTCTGAAGGCCCTTGAAGAGGCAAAAAATGAGgttacgggttttttttgtcttaaactttattgctcttcacttgttgaggatgttagttttaaaatatattactctcttgatgggcag

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgtt----cagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag
||| |||||||||||||||||  | || |  |||||| |    || ||||||||||| ||||||||||| || ||||| || || || || ||||||||||||    | ||  || |  || ||    | | | |  | ||| |                                          
CATCATGGATTTTGTCTCCGGCACTGCAAACCAAAACCTGGAGCTGCTGCAAGAGTTTTACCAGACAACGCTCAAAGCTCTCGAGGATGCCAAGAATGAGgttgtgccggtggctcgtgtt-tcttgctaatagtgatttgtgcag----------------------------------------

upper sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 4
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttcttgcct---tatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag
||| |||||||||||||||||  | || |  |||||| |    || ||||||||||| ||||||||||| || ||||| || || || || ||||||||||||  |  | | |      | ||    | | | |  | ||| |                                          
CATCATGGATTTTGTCTCCGGCACTGCAAACCAAAACCTGGAGCTGCTGCAAGAGTTTTACCAGACAACGCTCAAAGCTCTCGAGGATGCCAAGAATGAGgttgtgcctatggttcgtgtttcttgctaatagtgatttgtgcag----------------------------------------

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|6431605|gb|AU081257.1|AU081257
EST:     AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAG                         AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
genomic: AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttc ... tgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
EST: gi|55827482|gb|AU032236.2|AU032236
EST:     ACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAG                         AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
genomic: ACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttc ... tgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
EST: gi|3107821|gb|D43561.1|D43561
EST:     AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAG                         AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
genomic: AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttc ... tgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
EST: gi|86532861|gb|CI173067.1|CI173067
EST:     AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAG                         AGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG
genomic: AAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttc ... tgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTATGGATTTTGTCTCCGGATCAGCTAGTCAAAACTTCTCTCTTCTGCAAGAGTTCTACCAGACAACACTGAAAGCACTTGAAGAGGCAAAGAATGAGgttcagtttcttgccttatccaaattagaattttatgtaccaaaagattgttctttataccttgctattctttgctgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA