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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaaatttgaagttttgccaaagtatgcgtaaccactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG

Basic information

species Oryza sativa
transcript LOC_Os12g01390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 3
gtacaaaatttgaagttttgccaaagtatgcgtaaccactttgtttaaattgta-tcctataatcttaatgtattctttgcatattttattttctt--ttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG---------------------
||||||||       |  | |    | || | | |    ||| | ||  |  || |  |||   ||| | |||       ||| || ||| |  ||  |   ||| |||||||||| |||||||| |||||||| || || ||||||||||| || ||||||||||| ||||| |||||||| ||||| |                     
gtacaaaacactctctgatactgttgcat-cttgatgtttttctgtagctgttaattatatgcccttcaagta------acatgttctatatatttaatcttcaaccacagGTTGTATTTTGGAAGTGGATCACTCCCAAATTGTTGGGTTTAGTGACACAAACATCTGTTTACCACTGGTCGATTGAAGGTGATTCTGAGCCCACCAAGA

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 3
gtacaaaatttgaagttttgccaaagtatgcgta-accactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
         |    ||| |||   ||| | |  | || | |  ||     ||| |   |  || ||  || || || |||   | |   | |  ||||||      ||||| || |||||||| ||||| ||||| |||||||||||| | |||||||| || || || || || ||||||||||| |
--------gtaactgttatgctcgagtgtacaaacactattaagtgatggttg-acaatgaaaactctat-taatccttgtggaatgc-tctaattttcatg--tgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTATTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
gtacaaaatttgaagttttgccaaagtatgcgtaaccactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
         |    ||| |||   ||||| |  || ||||    ||||    |     || ||   ||     |   | ||  |   ||  |||  |  ||    ||||| || |||||||| ||||| ||||| |||||||||||| | |||||||| || || || || || ||||||||||| |
--------gtaactgttatgcacgagtatac--aaacact---attaagcgatggttgatgatgaaaactctattaatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtacaaaatttgaagttttgccaaagtatgcgtaac-cactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
            | | | |  ||  |  |     |  ||    |  |  ||||| || ||| |   |   | | |      | | || || |   ||  | |||  | ||     | ||||||||| |||||||| ||||| || |||||| |||||||  |||| ||||| |  || || ||||| ||||||||||| |
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgttt----ttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG

upper sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 3
--------gtacaaaatttgaagttttgccaaagtatgcgtaaccactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
         | |     || ||   || | | ||  ||  |   |  ||| | | | |  |||  | ||||||| |  ||   | |||  | |    || |||         | ||||||| |||||||| ||||| ||||| ||| || ||||  |||| |||||||||||||| | ||| ||||| ||||| |
gtgatgacctgccctccttaaatgctttcaatagattgaatgtac-ttttctattattattattttttaatcttgac-taagttctgctcactcctgttccttgctgtttggatagGTTGTCTTTTGGAAGTGGATTACCCCTAAGATGCTGGGCCTGGTTACACAAACATCAGTATTTCATTGGTCCATTGAAG

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), 75 (downstream exon)
Score: 108

CTCAAATACCTGGGACAACACAGGATCACCTGCAAATCTTCAACATTGAGGCTAAAACAAAAATTAAGTCCCACCAGATGCCTGAGCAGgtacaaaatt ... acaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
         tcttaat  putative branch site (score: 108)
                              ttttattttcttttca  putative PPT
     ataatcttaatgtatt  TA-rich tract