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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g52630.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G147849_T01 (Zea mays), 5'ss of exon 5
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag
| |||||||||| || || || || || || || ||||||||||| |||||||| |  |||||||| | ||||||||||||||| ||||| |||||||||||||    || ||    |  ||| | | ||   |||   |||||||||| ||    |||  |  |      ||| |   || ||||||||
TTTATACAGCGACTATCTTGAAGCGGCTGACACGCCTGGGTGGTACTGTGGACCGAACTTCTACACCATAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaatcgttcttcttaactctccttaggtgcccaaccttacattagcagagaa-agtgggtcggtagttaaaatctgctcgatttgcag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G110735_T01 (Zea mays), 5'ss of exon 5
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaag-gttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag
|||||||||||| || || || |||||||| || ||||||||||| || |||||||  |||||||| ||||||||||||||||| ||||| |||||||||||||  |  |||||    |||||||  ||||   ||| | |||    |   |||    |  ||     |   ||| |  || |||||||||
TCTATACAGCGACTATCTTGAAGCTGCAGACACGCCTGGGTGGTACTGCGGACCTAACTTCTACACCACAGAAGTCCTCCGCAAGTTTGCCAGGTCACAGgtaaaagcattgttcttaatgctctcaaagtgcccaacg-tac---ggggaagtgaaattgatagttaaattaaatctgttaaatttgcag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G00710.1 (Glycine max), 5'ss of exon 3
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaag-gttttgttgcccatgctct---------tga-agtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag----------------------
||| ||||| ||||| || |||||||| ||||||||||| |||||||||||||| | ||||| | | || || ||||| ||  | ||||||| | | |||||  | | |  | |||   |  |||         ||| | || | | |  ||    |  | | |      | |    |  |         | ||| |                          
TCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCGACTGATGTCCTTCGAGACTTTGCAAAGACCCAGgtgggtgctacggtgctagtattctgctccttaatgataataattataattatgaaaagaaattcttacaagtcaagcggctgtctgggctaaatatctttttcttttcccttttctgtgtag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G13080.1 (Glycine max), 5'ss of exon 5
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag----------------------------------------
 || || || ||||| || |||||||| ||||||||||| |||||||||||||||| |||||   | || || || ||||| || ||||| | | | |||||  | |  | |||  | | || |   ||   | |   |||    | | ||  ||   | | | |  |   | | | ||   |  || |                                         
CCTTTATAGTGATTATCTTGATGCTGCTGATACACCTGGATGGTATTGTGGACCTAATTTCTTTTCAACTGATGTGCTCCGTAATTTTGCCAAGACCCAGgtgtg-tgatattgtgc-tactttaagagagatgatgtctatggcatc-caactcttcgtaat-gttaatgatatcactaagaggtgtatggactaatttttcttttcccttttgtcggtgtttttgcag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G40090.1 (Glycine max), 5'ss of exon 3
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaaccct--tcaatttgcag
 || ||||| ||||| || |||||||| ||||||||||| |||||||||||||| | ||||| | | || || || || ||  | ||||||| | | |||||  |   | |||  |    |  |   | || |  | | |  | ||  |  ||  ||   | |   |   |     | |  | | |||| ||
CCTTTACAGTGATTATCTCGATGCTGCTGATACACCTGGATGGTATTGTGGACCCAATTTCTTCTCAACTGATGTTCTTCGAGACTTTGCAAAGACCCAGgtgggtgctagttttctgctccataataataat-gatgatgtaatacaagtgtctgggctaataatctttctctgtcttggtgattttgtag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G02160.1 (Glycine max), 5'ss of exon 5
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag------------------------------------
 ||||| || ||||| || |||||||| ||||||||||| |||||||||||||||| |||||   | || || || ||||| |  ||||| | ||| |||||  | |  | || |   | || |   ||   | |   |||    | || | |      ||| | |  |  |  ||  |    | |   |                                    
CCTATATAGTGATTATCTTGATGCTGCTGATACACCTGGATGGTATTGTGGACCTAATTTCTTTTCAACCGACGTGCTCCGTAGCTTTGCCAAGTCCCAGgtgtg-tgatatt-ctgctactttaagagagatgatgtctatggcatcaaactcttcctaatgttat-cgtatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcag

upper sequence: LOC_Os03g52630.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G49720.1 (Arabidopsis thaliana), 5'ss of exon 5
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttga-agtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaat----ttgcag---------------------------------------------------------------------------
||||||||| ||||| ||||||||||| ||||| ||||| ||||| |||||||||| ||||||  | |||   || || ||  | ||||| || || ||||||  | ||  || ||  | ||||| | || | |   |    ||     |    | | | |  |  | |    | ||  || |      ||| |                                                                            
TCTATACAGTGATTATCTGGATGCTGCTGATACTCCTGGATGGTACTGTGGACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttgacatctaaattggatttaactcggccttgctgtattttggcag

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|58670607|gb|CK059293.1|CK059293
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATG
EST: gi|2280737|gb|C25232.1|C25232
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27576324|gb|CA999018.1|CA999018
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGT
EST: gi|29639819|gb|CB644828.1|CB644828
EST:     ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29674436|gb|CB670711.1|CB670711
EST:     CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29624498|gb|CB629509.1|CB629509
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29639818|gb|CB644827.1|CB644827
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|58663082|gb|CK051768.1|CK051768
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629441|gb|CB634450.1|CB634450
EST:     ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|27578175|gb|CB000870.1|CB000870
EST:     CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: CTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|38469334|gb|CF953465.1|CF953465
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29629254|gb|CB634265.1|CB634265
EST:     GTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|396941140|gb|HO188349.1|HO188349
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29623193|gb|CB628204.1|CB628204
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29643849|gb|CB648856.1|CB648856
EST:     ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: ACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29630277|gb|CB635286.1|CB635286
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29673808|gb|CB670083.1|CB670083
EST:     GCAAATTTGCAAGGTCACAG                         CTCGATTATGTCTTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|163926677|gb|EG713693.1|EG713693
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
EST: gi|29668386|gb|CB664661.1|CB664661
EST:     GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAG                         CTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT
genomic: GACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggtttt ... caatttgcagCTCGATTATGTCCTAGGTAAGAACCCACTGAAGATGAGCTACGTTGTGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATACAGCGATTACCTGGATGCTGCAGATACACCTGGGTGGTATTGTGGACCTACTTTCTACACTACAGAAGTCCTCCGCAAATTTGCAAGGTCACAGgtaaggttttgttgcccatgctcttgaagtagtcaaagctacattagcacagttcggtgaatttgacacccaaaacccttcaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT