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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA

Basic information

species Oryza sativa
transcript LOC_Os01g73790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 3
gtatgtcaaccagtcccttt---------ctgagaataatatacctccattt-cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
||||||  ||  ||   |||         ||||| ||  |   | |   ||| |   || | | || |||| | |||||| |||           |||||||||||| || || || |||||  |||| ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||| |||||||||    ||||||
gtatgtgcacttgtttttttatttattttctgagtatggttggcttaattttgcaccatag-cattcttctgagaagatgcatg---------gttttgcagAATCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
gtatgtcaaccagtccctttctgagaataatatacct--ccattt---cgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
||| ||   |  ||  |||  |||| || ||   | |    ||||   |   ||| ||  | |||||| |||||| | |   ||||||  |||||||||||| || ||  | |||||| |||| ||||||||||| || ||||| |||||||| ||||| ||||| |||||||| || ||||||||     ||||||
gtaagtgttcttgtttcttggtgaggatcattatcttaattatttatgcaccatgttcagtcttctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
--------gtatgtcaaccagtccctttctgagaataatatacctccat-ttcgttatggtcgttt--ttctcataagatgtatgtcgccaatgaattt---gcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
          || |  |      | ||  | |   |  ||||  |   | || || |   |  ||   |  | ||   |  ||| |     ||   |||   | |||||||||| ||  | |||||||| || ||||| |||||||| || |||||||| |||||||| || ||||||||||| |||||||| ||    |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 5
---------gtatgtcaaccagtccctttc--tgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
          ||  |   | | | | |||   |||   |  |  |  |      ||   |  |     ||     ||  | | |||   |  |   | |||||||||| || ||  | |||||||| || ||||| || |||||||||||||||||||| ||  |||||||||| ||||| |||||||||||    |||||||
gtcagttacttacttttgctattgctttttgttgaagtttgttgatattttagccggagttttgaaaatttgttcaaattttctgttttcctttg-tctgcagAATCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 5
--------gtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgttt--ttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
          || |  |      | ||  | |   |  ||||  |     ||| |||  | |  |  |  |  |||    | | ||         | || |||||||||| ||| | |||||||| || ||||| ||||||||||| |||||||| |||||||| || ||||||||||| |||||||||||    |||||||
gtgagtttacattttgatttagactttgtttaagcttgtatatatgttactcgatatttttggataatgattctaaatattttctccattccttttctgtagAATCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 5
gtatgtcaaccagtccctttctga-gaataatatacctccatttcgttatggtcgtt----tttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
||  || |   | |     | ||  |||   | ||  |   ||| |  |  ||  |     ||| |   ||  | | |||   |  |   | |||||||||| ||  |  | |||||||| || ||||| || |||||||||||||||||||| |||||||||||||| ||||| |||||||||||     ||||||
gtcagttacttacttttgctatgttgaagtttttagatgattttagccagagttttgaaaatttgttcaaaattttctgttttcctttg-tctgcagAATCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtcaaccagtccctttctgagaat-aatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
||| ||   | | |||   | |   |   |||     ||  | |   ||||   | ||||     |     |   || | |   |  || |||||||| || ||||| ||||| || || ||||| ||||||||  | || ||||||||||| || ||||| || ||||| ||||||||||| |  |||||||
gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaagctttt-----agttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
    || |     ||    ||||  | ||| ||       | |  || |  |  || ||   |       |          |        |||| || || ||||  ||||| || || ||||| ||||||||||| ||||||||||| ||||||||||| |||||||| |||||||| ||    |||||||
----gttagtt--tcaacatctgtca-taacatttagtagtattttttttctttttcttactactgatcttgctctttttctcccacaatagAACCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtcaaccagtccctttctgagaataatatacct--ccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
||  ||    ||    || ||  |  ||    |   |     | |  || |  |  ||||| ||        |          |      | |||| || || ||||| ||||| || || ||||| ||||||||||| ||||||||||| |||||||| || |||||||| |||||||| ||    |||||||
gttagtt--tcaacatctgtcataacatggcttgtttggtagtatttttttcattttttttgtctctgatcttgctctttttctcccaccgtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA

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|58677005|gb|CK065692.1|CK065692
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTAGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58675034|gb|CK063721.1|CK063721
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58587635|gb|CF985943.1|CF985943
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGGCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58587411|gb|CF985719.1|CF985719
EST:     TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|25801443|gb|CA757404.1|CA757404
EST:     CTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
genomic: CTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG
EST: gi|58655446|gb|CK044126.1|CK044126
EST:     TTGATGGTCCTAGTGAGGGTG-TCCTCGGGTTTTGGCATGTTTCAGTAAC                         AATCTCCTGCGTCGGGAGCCCCTGAAGGTTGTTGATGGTGGCCAGTCCCAG
genomic: TTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAG

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: 71 (upstream exon), 51 (downstream exon)
Score: 16

TGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGAGGGTGTTCCTCGGGTTTTGGCATGTTTCAGTAACgtatgtcaac ... gaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
                                          aatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcaaccagtccctttctgagaataatatacctccatttcgttatggtcgtttttctcataagatgtatgtcgccaatgaatttgcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT