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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os04g54640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 7
gtaactctgtcaaactcgctatgcttgtagtctgtattgt---atttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
||||| || |     |  | |||| |||| |||  | | |   |  | |   | | |  |||      |   | |  |    |||||||| |    || |||       | || |             | ||   ||  |||||   |  ||  | ||| | |   | ||    | ||   |||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||||
gtaaccctctt---ttttccatgcatgtaatctacagtttttaacctgtccatgcctgtaatatacagtgggtagcttggtgttcatagtgtaaagttgaactttgcactgcacacc-tgcaaaaaagtcactaggatcaaacaagtatgaaagctactgacacctacaatttttgttc--tcagGTTAGCTGTAGTTTCAATGGCAGGACTGGCTGCTGAAGGTCTAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG

upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 7
gtaac-tctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatata--caaattacatgtgctcattacactgacgaaacatccaaaaacaccactaa-aataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
|||   | | |  | |   |    ||| | |    |||   || |          | |  ||||   | |   ||| |  ||   ||   |   | | |  ||||   |  |  ||||          || |  | | |||| |   | |      | ||  |||  | ||   || |  |||||| || ||||| ||||||||||| || || || || |||||| ||  ||||||||| || || |||||||| || ||||||||||  || |||
gtactatttatttaccatacacctcttattgctcttatccaatgtgagagaaaa-aaagccatgacaact---tataacttttcaagaaccaagtaccaaccaaaccaagccttattaatcacaaaacttgcctttaagaaatacgaagagttgtaattagtaatttaaaaaaaat-tcatatcagATTGGCTGTTGTGTCAATGGCTGGACTGGCAGCAGAAGGTTTAACATATGACAAGGTGGTTGGTCAATCTGCTGATCTTTTCAGTCTCCAG

upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 7
gtaactctgtcaaactcgc-tatgcttgtagtctgtattgtat-ttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacact-gacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
       |||  |  |  | ||  | | || | | | || |    | |        | |  ||||   | |   ||| |  ||   ||   |   | | |  |||     |||     |  |  |||  | ||| | |  || |   || |     | | |   |  | |    | |  |||||| || ||||| ||||||||||| || || || || |||||| ||  ||||||||| || || |||||||| || ||||||||||  || |||
------gtgtttatttaccatacacctctaatttctcttattcactgtggaagaaaaaagccatgccaact---tataacttttcaagaaccaagtactaaccaagc---caagcctta-ataatcacaaaacttggcttaatagg-aagagttttaattagtaatttcatttttttcatatcagATTGGCTGTTGTGTCAATGGCTGGACTGGCAGCAGAAGGTTTAACATATGACAAGGTGGTTGGTCAATCTGCTGATCTTTTCAGTCTCCAG

upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 7
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaata-tacaaattacatgt--gctcattacactgacgaaacatccaaaaacaccactaaaata--aataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
                                                                                          | || |  || | ||| | |  ||||    |  | | |||  | | | |  |  | |    | ||  || | ||   |        | || |  |||||| || || ||  ||||||| || || || || ||||| ||  ||||||||||||| || |||||||| || ||||||||||| ||||||
---------------------------------------------------------------------------------------acataatcctccatagatagttcggattatggattagttaatttaaattaagggaattgccggtagacagctgacattccacctttaactgttattccagGTTGGCGGTTGTAGCAATGGCTGGACTTGCAGCAGAAGGCCTGCAATATGACAAAGTGGTTGGTCAATCTGCCGATCTTTTCACTCTTCAG

upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ34800 (Selaginella moellendorffii), 3'ss of exon 6
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
                                                                                                                              ||     ||   |  |||       |   | || |   |  |   |||||||||||| | ||||| || |||||||| ||||| ||||| || | |||| |||||||||||||| | || || || || ||| | ||| ||||||||
-----------------------------------------------------------------------------------------------------------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttc---tattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCCCTTCAG

upper sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ23530 (Selaginella moellendorffii), 3'ss of exon 6
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
                                                                                                                              ||     ||   |  |||       |   | || |   |  |   |||||||||||| | ||||| || |||||||| ||||| ||||| || | |||| |||||||||||||| | || || || || ||| | ||| | ||||||
-----------------------------------------------------------------------------------------------------------------------------gtatctgaactcgaactcctttctttcttttgaagtttctttc---tattgtatcagGCTGGCTGTCGTTTCAATGGCTGGGCTTGCTGCCGAGGCTCTAAAATATGACAAAGTTATTGGCCAGTCTGCCGATTTATTCTCTCTTCAG

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|88511232|gb|CI438738.1|CI438738
EST:     TTGCAAAAGGTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTTTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88508320|gb|CI435826.1|CI435826
EST:     TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTNTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|38476935|gb|CF961068.1|CF961068
EST:     TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88548468|gb|CI476843.1|CI476843
EST:     CAAAAGCTAATATACAGTGGCCAGCTTGATCCAAAGGAGATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTGTAGAATATGA
genomic: CAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88472793|gb|CI410064.1|CI410064
EST:     TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88281159|gb|CI402357.1|CI402357
EST:     TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88975471|gb|CI023722.1|CI023722
EST:     TTGCCAAAGCTAATATACAGTGGCCAGCTTGATCGAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88521051|gb|CI448705.1|CI448705
EST:     TGCCAAAGGTAATATACAGTGGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGGTCNCTGCTGAAGGTGTAGAATATGA
genomic: TGCAAAAGCTAATATACAGT-GGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88470272|gb|CI407543.1|CI407543
EST:     AAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTGTAGAATATGA
genomic: AAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88510874|gb|CI438380.1|CI438380
EST:     TTGCAAAAGGTAATATACAGTGGCCAGCTTGACCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTTTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88527421|gb|CI455579.1|CI455579
EST:     TTGCAAAAGGTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTANTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88971502|gb|CI017816.1|CI017816
EST:     TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
genomic: TTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA
EST: gi|88474642|gb|CI411913.1|CI411913
EST:     ATACANTGGCCAGCTTGATCAAAAGGAAATAGACAG                         GTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGGTGAAGGTGTAGAATATGA
genomic: ATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGA

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: 69 (upstream exon), 37 (downstream exon)
Score: 15

GATATTCCTTGGACATTGGAAAGGAGCATGTTAACTTGATAGATGATCAATTGCAAAAGCTAATATACAGTGGCCAGCTTGATCAAAAGGAAATAGACAGgtaactctgt ... attgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG
                                  aaataac  putative branch site (score: 15)
                          actaaaataaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactctgtcaaactcgctatgcttgtagtctgtattgtatttattttttcttagaatcatgtttattttgtatcagcttcatagtttctgattcaacacaaatatacaaattacatgtgctcattacactgacgaaacatccaaaaacaccactaaaataaataacggatattgtatcagGTTAGCTGTAGTGTCAATGGCAGGGCTCGCTGCTGAAGGTCTAGAATATGACAAAGTTGTCGGTCAATCGGCAGATCTTTTCACCCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT