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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtaggaagCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGATGAGC

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 1
--------------tttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtaggaagCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTA---ACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGATGAGC
                |  |  |||| |   || | |    |  | ||   | | ||| | ||||||        ||   ||||  |||||   |||||| ||||  ||| |||  | | ||||||  |||||  ||||||||||||| ||||||||   |||||||||||||||| ||||| |||||||| |||||||| ||||  |||       
actgctacagagtaccttctcttttgaaaagtactggcacttttttat--catttattattgttatta-------atcgcttgagttgattt-gagttttccgttcatagCAAGTACCTATTATCAACCATGTTTGGACGCATGCCAAGGAAGAGTAGTAACAATACCAAGTATTACGAGGTTCTTGGTGTGTCTAAGACCGCAAGTCAG-------
















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|29673001|gb|CB669276.1|CB669276
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58655503|gb|CK044183.1|CK044183
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58666150|gb|CK054836.1|CK054836
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58658345|gb|CK051083.1|CK051083
EST:     GGTGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: GG-GCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58601753|gb|CK012281.1|CK012281
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58663897|gb|CK052583.1|CK052583
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58604589|gb|CK015117.1|CK015117
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58602101|gb|CK012629.1|CK012629
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58664824|gb|CK053510.1|CK053510
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         CCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACC
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaagCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACC
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58679094|gb|CK067781.1|CK067781
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|33796281|gb|CF324007.1|CF324007
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     GGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: GGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|88343932|gb|CI654968.1|CI654968
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58660176|gb|CK048856.1|CK048856
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     GCTTCTTCCTCTTCCGGAAG                      
genomic: GCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|29631437|gb|CB636446.1|CB636446
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGGAAG                      
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCC----Ggtgaggaagc ... ttgtagg
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-
EST: gi|58600729|gb|CK011257.1|CK011257
EST:     CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCG                         G
genomic: CGGGCCGTCGTCTGGATCTGATCTAGGAGCGGTCGCTTCTTCCTCTTCCGgtgaggaagc ... ttgtaggaag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttattgcttcatgatttgttgatctgattccaagttttacgtttgtaggaagCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGATGAGC
                        atctgat  putative branch site (score: 4)
                                  aagtttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctttgtttgcaggatattagtttgtactaatgctactcattgtagttattgcttcatgatttgttgatctgattccaagttttacgtttgtaggaagCCCTTTTTATCAGTCATGTACGGACGCATGCCAAAGAAGAGTAACAATACCAAGTATTATGAGGTGCTTGGTGTATCTAAGACAGCAACCCAGGATGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - tgtttgc
- - - - - - - - - - - - - - - - -tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc