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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT

Basic information

species Oryza sativa
transcript LOC_Os01g52390.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G116282_T02 (Zea mays), 3'ss of exon 5
ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgt----------tccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT
     | ||    ||||||  |     ||  | ||  | |    | ||||  |  | || |||||||||  || | || || || ||| | ||||          | ||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||| |||||||| |||  | || 
-----agttccatgatattttttatggttatgttt--ttgtgg-ttaattcttagttgagaaaaaaact--gggtgctgatgtgataattattgtaatcttggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTACGGCGGCCGTGGCCGTGGAAGGGGCCGTGGGGATCGTGGTGGTTTTAGAG

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G055276_T02 (Zea mays), 3'ss of exon 4
--ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgt--tccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT
  | |||  ||  |   |||     | ||||| | || ||     || | || |      |||             |  ||||      ||| |||   | ||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||| |||||||| |||  | || 
atgatgtttttgattcttatgttatgtttttgtggttaatg----cttagttgagaaaaaaaactgggtgctgatgtgataattatcgtaatcttggggtgcagTCGGTGAGCATCAACGAGTTCCTGAAACCTGCTGAAGGAGAAAGGTACTACGGCGGCCGTGGCCGTGGAAGGGGCCGTGGGGATCGTGGTGGTTTTAGAG

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA03G26100.1 (Glycine max), 3'ss of exon 6
ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattt--tgttc-cagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTA---TGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT
  ||| || |  || |  |  |   |||||   |  ||     ||   ||||| ||  |             |||||| || |   || |||  | ||| |||||||| | ||||| |||||| |||||||| || ||||| |||||||||||   ||| || |||||||| ||| | || |||||   | | || |||       
--tgttatgaaaggttcatattctgttttgtt-tccatgtgccctggttttatatttcattctcctgactttgtttcttatattggaattttcttattctcagTCTGTCAACATCACTGAGTTTCTGAAGCCAGCTGAAGGGGAAAGGTACTACCCTGGTGGGCGTGGTCGGGGACGTGGCCGTGGTTCTAGAGGAGGTTACA---

upper sequence: LOC_Os01g52390.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0620g00020.t01 (Vitis vinifera), 3'ss of exon 6
----ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT
         ||  |    | ||  |  | | | |    ||| |||||   | || ||             | | |  | | | ||   ||   ||| |||  ||||||| ||||| ||||||||||||||||| || ||||| || ||||||||||| || |||||| | ||  | || |||||     | || ||   || | 
ataaaaaaaaaccaaaaaaaatgacctggtgtagatgctga-agcaatatatttcattccaattttgttga-tgatatgtttgattgcttg--tttggttgtagTCTGTCAGCATAAATGAGTTCCTGAAGCCAGCTGAAGGGGAGAGGTACTATGGTGGTCGTGGTAGGGGTCGTGGCCGTGGTACAAGAGGAGGATTTGCAG

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|8335069|gb|BE040053.1|BE040053
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|55411490|gb|CV723866.1|CV723866
EST:     GAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: GAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|86836624|gb|CI347277.1|CI347277
EST:     GCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAACATCAATGAGTTCCTTAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: GCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|218486753|gb|FG965219.1|FG965219
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAA
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAA
EST: gi|218493559|gb|FG968382.1|FG968382
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|157652089|gb|EX451723.1|EX451723
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGANCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTAC
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTAC
EST: gi|66913583|gb|CX100431.1|CX100431
EST:     CCAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|58679736|gb|CK068423.1|CK068423
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|58599621|gb|CK010149.1|CK010149
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|88830569|gb|CI078013.1|CI078013
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|29686653|gb|CB682928.1|CB682928
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|55411837|gb|CV724213.1|CV724213
EST:     TGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: TGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|29614482|gb|CB619495.1|CB619495
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|300216202|gb|HO087987.1|HO087987
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|38469519|gb|CF953650.1|CF953650
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|218486771|gb|FG956353.1|FG956353
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
EST: gi|163928222|gb|EG714626.1|EG714626
EST:     ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAG                         TCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT
genomic: ACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTAT

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: 75 (upstream exon), 36 (downstream exon)
Score: 8

GGTTCTGACAAGGATAAGAAGAAGGAAAATGCTGAGCGCGATGAGCGTGCCAAGAAGgtattttaac ... tttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT
                             ttctaat  putative branch site (score: 8)
                                            ttttgttcc  putative PPT
                                taatctgttaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtaattattggatattcctagattttgcgattgatagcaactcaatttatcttggaaaaaaaaactcaggtttctaatctgttaaattttgttccagTCTGTGAGCATCAATGAGTTCCTGAAGCCTGCGGAAGGAGAAAGGTACTATGGCGGCCGTGGTCGTGGAAGGGGGCGTGGAGATCGTGGCGGTCGTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - attttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtta