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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccataactcatttgtttcttcagggttttagtgaacgaatgtcattacttacatctgaacctttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC

Basic information

species Oryza sativa
transcript LOC_Os12g07740.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G117900_T01 (Zea mays), 3'ss of exon 8
------------------------------------gtttgccataactcatttgtttcttcagggttttagtgaacgaatgtcattacttacatc--tgaaccttt--cacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC
                                      | |  ||||    |   |  || |  | | || ||| | ||   | |  |  ||  ||  ||| | |||      |||||||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||||| |||||||| || |||||||||||||| || ||||||||||
gtttgtaaaaatatttgcttcttcatgatatagatgaatagaaataatatctccttcactacctgatgtttgtgta-gagctttaggaggtatgtcattgagcatttgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGCGAGATCCTCATGC

upper sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 8
gtttgccataactcatttgtttcttcagggttttagt-------gaacgaatgtca---ttacttacatc--tgaaccttt--cacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC
|||||   |||    |||| |   ||| | ||||||         ||    ||| |   |||  ||  ||  ||||| |||      |||||||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||||| |||||||| || ||||||||||||||||| ||||||||||
gtttg---taaaatctttgctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGTGAGATCCTCATGC
















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|89161809|gb|CI102157.1|CI102157
EST:     TGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: TGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|33808097|gb|CF329938.1|CF329938
EST:     TGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: TGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|5038797|gb|AU070907.1|AU070907
EST:     AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|9865948|gb|AU101698.1|AU101698
EST:     GGTTCTGGGTGAAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: GGTTCTGGGTG-AAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|29640632|gb|CB645641.1|CB645641
EST:     AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCCCA
genomic: AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|88689622|gb|CI733198.1|CI733198
EST:     AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|88902778|gb|CI088316.1|CI088316
EST:     TGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: TGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|86498770|gb|CI141403.1|CI141403
EST:     AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: AGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
EST: gi|88841207|gb|CI080661.1|CI080661
EST:     TATGTGGAGCTTGAG                         ATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA
genomic: TATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 70 (downstream exon)
Score: 16

TGGAACAACCATGGATCCAACTTTGACACGTGCCGATAGACTGGTTGGGCAGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccata ... tttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcagggttttagtgaacgaatgtcattacttacatctgaacctttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC
                             tacttac  putative branch site (score: 16)
                                           cctttcac  putative PPT
                           attactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccataactcatttgtttcttcagggttttagtgaacgaatgtcattacttacatctgaacctttcacacagATCAACTTCTTCCTTCTTCGGAGGCTATTAGGTGTGAGGACAAAAGGCACAGAGAAGGCTGGGAAGGTCTCCAAGCTCACCAAGGGTGAAATCCTCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA