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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG

Basic information

species Oryza sativa
transcript LOC_Os04g56530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 1
gtgagtgttc-cggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
|||||  ||    | |||| || |||| ||||| || |||||||||||| |  || ||  ||||||||| ||  |    ||| |   | ||| || ||                    |||  |  ||||||||||| |||||||||||||||||||| || || || || || |||||||||||||||||||| ||||| || |||||||||||||| || || ||| |||
gtgaggatttatcgcgcctcccacctcagatccagg-ggaattcgtgtttttttgctgcgaattttggggtta-tcctactctcactcagtgcgcctg-----------------cacgggcccgtgtgcagATGCTTGGAGATGAAATAGGGAAGGGGGCGTACGGCCGCGTATACAAGGGGCTTGACCTGGAGAATGGCGATTTCGTGGCCATCAAACAGGTCTCGCTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
                        |  | |    | | | |||  |||    | || ||  |||   ||      |||     ||| |||     | | ||   |     |   |          || |||||||| |||||||| || || || ||||||||||| ||||| ||||||||  | ||  |||| ||||||||||| || || || || ||||| || ||||
------------------------ttagttttttg-gcagttcaggtttgattagt-ttggtttcaagtcg----tcggatcttgagtgt-cattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggt-gttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggt-----gcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
                                     || || |  | ||  | || ||||||  ||   ||||||||    |||    |   || |   |    |       | |  |  |    ||     ||||||||| || |||||||| || || || |||||||||||||||||||| ||||| ||| |||| ||||| || || ||||| || ||||| || ||  |||
-----------------------------------cagatttggcctcctacttgttgttaat--tgctattggtttcatgtactcgaggctggctttcatttctgcttttttgatccgacgaattgtatctggcagATGCTTGGTGATGAAATCGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGATTTTGTGGCTATTAAGCAGGTCTCACTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
                            || ||         |     |||||  | |   ||||        | |  ||  |  |    |||      |  |  |      ||| ||  ||  |  |||| |||| ||||||||||| || || || |||||||| ||||||||||||||  | ||  |||| |||||||| || ||||| ||||| || || ||| |||
--------------------------acatacgaactagcaacaatcgctggta-tctggcttttccagagactcttacttgc--atccagtgatgtaatatgatgtcatatggtttgatggttg--gcagTTGCTGGGAGATGAAATCGGTAAAGGGGCATATGGCCGAGTGTACAAGGGATTGGATTTGGACAATGGAGATTTTGTGGCGATCAAACAGGTTTCGCTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
           ||    |     |  |  |     ||  |||| |   ||    |||| |     |  ||| | ||  ||      ||  |||  | |     |       |  | |||         |||||||| || || ||||| || || || |||||||||||||||||||| ||||| ||| |||| ||||| ||||| |||||||| || || || || ||||
-----------gggatatgttctcctgcttgtttttgagattctttggctcaatgtgtca-----gaatttagcttttct-----gcta-gtgtcttgactttgaccaattgtatttgg---------cagATGCTTGGTGACGAAATTGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGACTTTGTGGCCATTAAACAGGTCTCATTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
|||||| || |  |  || |    |  | |   ||  ||  ||||| ||   |  |  | || ||  || | ||   | ||| |   |   |       ||    |        |||           |||||  | ||||||||||| ||||| || ||||||||  |||| ||||| ||  | |||||||||||||| ||||| ||||| || ||||| || ||  |||
gtgagtttttc--attctcctttttttggtttagg--gagatcgtgatc--attttcattatcttttgtatcgtgctgatcagtttttccttcttcttttgtatcg--------tgtaa----ttaaacagATAATAGGAGATGAAATCGGGAAAGGTGCATATGGCAGAGTTTACAAAGGCTTGGACCTGGAAAATGGGGACTTTGTGGCAATTAAGCAGGTTTCTCTGG

upper sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ14289 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
|||||| || |  |  || |    |  | |   ||  ||  ||||| ||   |  |  | || ||  || | ||   | ||| |   |   |       ||              |||    |     |||||  | ||||||||||| ||||| || ||||||||  |||| ||||| ||  | |||||||||||||| ||||| ||||| || ||||| || ||  |||
gtgagtttttc--attctcctttttttggtttagg--gagatcgtgatc--attttcattatcttttgtatcgtgctgatcagtttttccttcttcttttgtat----------cgtgtaatcaa--acagATAATAGGAGATGAAATCGGGAAAGGTGCATATGGCAGAGTTTACAAAGGCTTGGACCTGGAAAATGGGGACTTTGTGGCAATTAAGCAGGTTTCTCTGG

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), 72 (downstream exon)
Score: 43

GCCCGATCTCGGGGTGGGTGTGTGTGGGGGGCGGGGCGAGATGGCGTCGCGGCAGCACAATGCGCAGTTCCACAAGAACAAGACGCTCGACAACAAATATgtgagtgttc ... gccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG
    cactgac  putative branch site (score: 43)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG