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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgttttgttgttaatatgatcataatagcatgatagtaagttctcatgttaatttaacttttgcattcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTATTATGATGGGGACCTCCACTCAGCAAGAAGCTATTATGCGCGTTCGTTGG

Basic information

species Oryza sativa
transcript LOC_Os02g55200.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55200.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G049672_T01 (Zea mays), 3'ss of exon 5
gttgtgttttgttgttaatatgatcataatagcatgatagtaagttctcatgttaatttaacttttgcattcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTATTATGATGGGGACCTCCACTCAGCAAGAAGCTATTATGCGCGTTCGTTGG
||| | ||   || ||| | | |   ||||| |||    | || ||| |||| | ||||| ||||| || | |||| ||| |||| ||||||||||| ||||||||||||||||| || || ||| |||| |||||||| |||||||| || ||||||| ||||||||| ||||| ||||
gttctattcaatt-ttagtgtaactgtaataacatt---gaaatttcacatgctgatttatcttttacacttatctgcagCTGGTTCATACTCTCTCTGTTTCACTAAATAAAATCGGTGACCTTCGCTACTATGATGGCGACCTCCAATCTGCAAGAAACTATTATGCCCGTTCATTGG
















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|29657742|gb|CB654017.1|CB654017
EST:     ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
EST: gi|2427558|gb|C72021.1|C72021
EST:     ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
EST: gi|58589478|gb|CF987786.1|CF987786
EST:     GTGAAGAAAGTGCTGAATTCCTCTCGAAA-TGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: -TGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
EST: gi|218487528|gb|FG948329.1|FG948329
EST:     ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
EST: gi|29659820|gb|CB656095.1|CB656095
EST:     ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
EST: gi|8956748|gb|BE230551.1|BE230551
EST:     ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAG                         TTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT
genomic: ATGAAGAAAGTGCTGAATTCCTCTCGAAATTGCCCAAAAAGGATCTGGAGgttgtgtttt ... tcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatagcatgatagtaagttctcatgttaatttaacttttgcattcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTATTATGATGGGGACCTCCACTCAGCAAGAAGCTATTATGCGCGTTCGTTGG
                              atttaac  putative branch site (score: 3)
                                            ttcatct  putative PPT
                        atgttaatttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgttttgttgttaatatgatcataatagcatgatagtaagttctcatgttaatttaacttttgcattcatctacagTTGGTCCATACTCTCTCAGTTTCACTAAATAAAATTGGAGATCTTTGCTATTATGATGGGGACCTCCACTCAGCAAGAAGCTATTATGCGCGTTCGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC