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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgctacctttgtacattttacaaactgactagttgctgtgattgtttatattattctggctgtttatattattatgtttatattgcacattttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC

Basic information

species Oryza sativa
transcript LOC_Os03g42840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 6
-attgctacctttgtacattttacaaactgactagttgctgtga--ttgtttatattattctggctgtttatattattatgtttatattgcacattttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
  ||  ||| |   || ||  | |||||     |     ||  |  ||| | |   |||      | |  || |||||| ||||   || |   || || ||||| ||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||| ||||  | || ||||| |||||| |||| ||||||||||
gcttattacttaaataaatactccaaacaagtgaaaacgtgacaagttggtcagcctatgtgctatttgaatcttattaagttt---tttctttttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAATGGCGCAATTTAGTAGTGAGGCATCCCTCTTTATTGAAGAACATGACAC

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 7
attgc-tacctttgtacattttacaaactgactagttgctgtgattgtttatattattctggctgtttatattattatgtttatattgcacattttaca-agACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
| ||  |  || ||   | | ||  ||     | ||     | |||  || |  || | |     | | | | ||     | ||| | |  |  |||   ||||||||||||| || || || |||||||||||||| ||||| || ||||||||||| || || ||  |    ||||| ||  | |||||||| ||||| |
actgaatttctctgctaaatatagtaaaccttttgtcagccttatt-cttgtgctactataatcttctctgt-atgtcactgatagttcttaagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTC

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G01870.2 (Glycine max), 3'ss of exon 7
attgctacctttgtacattttacaaactgactagttgctgtgattgtttatattattctggctgtttatattattatgtttatattgcacat---tttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
     ||  | |||  | || |  |     | |      ||  ||  |  ||||||  |   | | ||||    |||   || | || || |    |    |||| || ||||| |  || ||||||||||||||||| ||||| || ||||||||||| || || ||  |    ||||| ||  | || ||||| ||||| |
-aaattatgtatgttgacttgaagattatgccatacaaagttctttgtgctattataatc-ttctctatagagctatcacta-actgtacttaaactcttcagACTTTCGAGGAAGTTGATACAAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCAGCATCCATCCCTTCTAAAAAATATGACTC

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
attgctacctttgtacattttacaa-actgac--tagttgctgtgattgtttatattattctggctgtttatat-tattatgtttatattgcacattttaca-agACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
     |   | |||  | || | ||   ||||  | ||   |   ||  ||  | |  | ||      || | | |||     | ||| | |     |||   ||||||||||||| || || || |||||||||||||| ||||| || ||||||||||| || || ||  |  | ||||| ||  | |||||||| ||||| |
-----tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC

upper sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 6
attgctacctttgtacattttacaaactgactagttgctgtgattgtttatattattctggctgtttatattattatgtttatattgcacattttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
 |   |   |  | |     |  |     |||   |   |   |||| | | ||           |||||   || | ||  | | |  |||| | | |||| |||||||| || ||||||||||||||||| || ||||| |||||||| ||| | |  || |||||  |||| || ||  |  |||| || ||||| |
ctccttggttaagcagcaagttgagggaaactcaatttggattttgtatttgttgcatccatctcttataacctttttttattttggtgcattgttccagACCTTTGAGGAAGCTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTC

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|13420903|gb|AU174993.1|AU174993
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTNAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|58589859|gb|CF988167.1|CF988167
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCGTCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|87021814|gb|CI277981.1|CI277981
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|86499115|gb|CI141748.1|CI141748
EST:     TGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: TGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|88577319|gb|CI673890.1|CI673890
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|218489708|gb|FG943932.1|FG943932
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|38475615|gb|CF959748.1|CF959748
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|86525849|gb|CI166055.1|CI166055
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATCGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
EST: gi|163926837|gb|EG710181.1|EG710181
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAA
EST: gi|163920409|gb|EG709563.1|EG709563
EST:     AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAG                         ACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA
genomic: AGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAA

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: 67 (upstream exon), 56 (downstream exon)
Score: 25

GTTAAGCAAATGGTTGTTGCAACACTTGCTGAGTCGGGAATGAATCTTTCGGATGAAGTCATAGAGAGCATCATTGATAAGgtaaacatga ... attttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatattattctggctgtttatattattatgtttatattgcacattttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC
                   tttatattattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgctacctttgtacattttacaaactgactagttgctgtgattgtttatattattctggctgtttatattattatgtttatattgcacattttacaagACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC

- tgctacc
- - - - - - - - - - -acaaact
- - - - - - - - - - - - - - - - -gttgctg
- - - - - - - - - - - - - - - - - - - - tgattgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tattgca