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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccgttacggcttataatcagtcgtaggcaaccgatggggacctacataaacttccacagcaggtgagataacatgaatgcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA

Basic information

species Oryza sativa
transcript LOC_Os02g57180.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G143651_T01 (Zea mays), 3'ss of exon 8
-------------------------gccgttacggcttataatcagtcgtaggcaaccgatggggacctacataaacttccacagcaggtgagataaca--tgaat-gcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA
                         |  |      || | ||| |||    ||||    |||    |||        |   | |     |  |  | ||  | |||  |    | ||   |||||||||||||||||||| |||||  | |||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||  || |||||||| || || 
gtaagttttgcctgttgactctcctgatgcctgacctgaaaatgagttcagggcatgaaatgacctccttttgttcatgttagaagttctttgccagcagttaaattacgtaatgttcccttttgcagGATTCAGCCTGTGTATGTAATCGATGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCT

upper sequence: LOC_Os02g57180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 8
------------------------------------------------gccgttacggcttataatcagtcgtag-gcaaccgatggggacctacataaacttccacagcaggtgagataacatgaatgcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA
                                                  | ||       | | | | | ||   |  || | |   ||| |   | | |||  | |     |    | |  |||   |||   |    || ||||||||| || |||||||||||| | ||||||||||||||  |         | | |||||||| ||||| ||||||||||| |  || ||||| ||||| |||
gtatgtataaatctattaggcaattactatgaacttcaatctttttttttctttttttaccaaagtgaattgtgttgttactggttctgacttctttcagctttgaaattcattttttttatctga---caaa--tgcaattattgcagGATCCAACCTGTTTATGTTATTGATGTTGCTGCTGCACTCACTTCACTCTTGAAGGATGATGGCACTAGCATGGGAAAAATTTATGAACTGGGTGGTCCA

upper sequence: LOC_Os02g57180.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G20360.1 (Arabidopsis thaliana), 3'ss of exon 8
gccgttacggcttataatcagtcgtaggcaaccgatggggacctacataaacttccacagcaggtgagataacatgaatgcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA
     |||| |||  | ||  |                 |    | |  |||||  |  | || |    |  | |      |||  |     |  |||||  | |||||||||||||| || |||||||||||||| |||||     | || |||||||| ||| |||||||||| || || |||||| | ||||| |||
----gtacgtcttgaattctttgtgcaattcttttcactggttcatagcaacttgaaatgtagatttagttccgtc--cctaacgataactctactgcagATTCCAGCCTGTTTATGTGGTTGATGTTGCTGCTGCGATTGTTGCTGCTCTAAAGGATGATGGCTCCAGCATGGGGAAAACATACGAATTGGGTGGTCCA

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|11442907|gb|BF430806.1|BF430806
EST:     TTTGCTAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|58690755|gb|CK079442.1|CK079442
EST:     TTTGCTAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|29673109|gb|CB669384.1|CB669384
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|29671359|gb|CB667634.1|CB667634
EST:     TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|8856604|gb|AU093922.1|AU093922
EST:     TTGGGGTTTCCNCCCCNCTTGTTGA-TCTGGGTCTAC-AA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTGGGGTTTCC-TCCCTCTTGTTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
EST: gi|88730417|gb|CI754030.1|CI754030
EST:     TTGATTCTGGGTCTACAAA                         GATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT
genomic: TTGATTCTGGGTCTACAAAgtaattgaac ... gtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaacttccacagcaggtgagataacatgaatgcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA
                     agataac  putative branch site (score: 3)
                                              tttttgc  putative PPT
                       ataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccgttacggcttataatcagtcgtaggcaaccgatggggacctacataaacttccacagcaggtgagataacatgaatgcaaccttttggtttttgcagGATTCAGCCTGTTTATGTTGTGGATGTTGCTGCTGCTATTGTCAACTCCCTCAAGGATGACGGCACCAGCATGGGAAAGACCTACGAACTTGGTGGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA