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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g15310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095114_T02 (Zea mays), 3'ss of exon 2
gtaaga----gaagatccgccgcttcg--cgctgtgcgtgg----tggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggttttt--ttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
||||||    |  |    ||  |||    ||  ||   |||    || || || | |  |  |  || |   |  | ||    | | ||       ||| |  | | ||||||||||||| ||||| || |||||||||||||||||  |||| || |                                                  
gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtgtgattattcgttcagtctattgtttatcctgagtcctgaccgttaaaactttttgtgttctcagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATT--------------------------------------------------

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
----gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttg-gtttggtt-tctgatcgg-ctagggtttga---aacttttg---tgtggttttt----ttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
    | | |  | |  |||  |     |    | ||| || ||| || | || || || || | ||   |||  ||| |     ||  |||   ||    | ||    | | ||||||||||||| ||||| || ||||| |||||||||||  |||| || ||||||||||||||||||||||| ||  |||||||||||||||||||||||
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 2
gtaaga----gaagatccgccgcttcg--cgctgtgcgtgg----tggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggttttt--ttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
||||||    |  |    ||  |||    ||  ||   |||    || || || | |  |  |  || |   |  | ||    | | ||       ||| |  | | ||||||||||||| ||||| || |||||||||||||||||  |||| || ||||||||||||||||||||||||||  |||||||||||||||||||||||
gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtgtgattattcgttcagtctattgtttatcctgagtcctgaccgttaaaactttttgtgttctcagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCACCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
----gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttg-gtttggtt-tctgatcgg-ctagggtttga---aacttttg---tgtggttttt----ttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG-
    | | |  | |  |||  |     |    | ||| || ||| || | || || || || | ||   |||  ||| |     ||  |||   ||    | ||    | | ||||||||||||| ||||| || ||||| |||||||||||  |||| || ||||||||||||||||||||||| ||  ||||||||||||||||||||||| 
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
gtaagagaagatccgc-cgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgt----gtggtttttttt----tagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
|| ||  ||   ||    ||||     |   | |  |  || || || ||   || |  |        || |  ||||| |||       ||||  |||     |||| ||||| || || || || ||||| || |||||||||||||| || || || || |||||||||||||| ||||| || || ||||| ||||| || 
gtgagtcaaaccccctgtgctttatttttaccctctttttttttagggttaccttattgttattatatgtgtagaacttgtgttaatactgtttgatttgtaacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
          |  | |   |||   || | |    |  || | |   ||  ||  |  |  | | | | | |  |  ||  ||   |  | |   || | ||||| || || || || ||||| || |||||||| ||||| || |||||||| |||||||||||||| || || || || ||||| || || || 
-------gcaactcact-tttcattctcttctcttttatt-tctaactta-ttattattatgatggtgatggtgatgttgatg--atgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------gtaagagaagatccgccgcttcgcgctgtgcgtggtggttg---tttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
                                     ||   ||||    || |  |     || || | |   | |   | |        |||   |         |||||| |||    ||  | ||||  |||||||||||||||||||| || ||||| ||||| ||||| |||||||| || || || |||||||||||||| || || || || || || || ||||||
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatctt----gttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
--gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaactt---ttgtgtg-gtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
    |   ||| |   || |   | || |||      |   | |  |  || |  ||| |        |   || |||||    ||  ||  | || |  ||| | ||||||||||| || || || || ||||| ||||| ||||| ||||| || || ||||||||||| || || ||||| ||||| || |||||||| 
cctcagatgaaaacaagcagagcctcgatgta-aaattttctttaagagttagcatctcact--tcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------------------------------------gtaagagaag-----atccgccgcttcg--cgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
                                                                             |  ||| ||      | | |  ||     |  | |   |  ||  |||| || | | |   ||      |  ||| | | |       || | |  | |  |||| || ||||| || || || ||||| || ||||| || || || ||||| || || ||||||||||| ||||| || || ||||||||||||||||||
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagatagaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatatcctgcatgtt-ggatcgttacatggatcttttaggtctaacatgacctcgtcggtaatctgcagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG

upper sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG-
                           ||| ||| || || || | ||   | | ||           | ||||| ||   |  |||        |||| |||||||| ||||| || ||||| ||||| ||||| ||||||| |||||| |  |||||||||||||| || || || ||||||||||| || ||| 
---------------------------gtgagtgatg-ttcttcgtttccttctttg-----------tctgaaaattcgcttgggt--------agCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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: 72 (upstream exon), 43 (downstream exon)
Score: 44

CTTCCGCTCTCGCTCCTCAAGACCGCCCAGGGGCATCCCATGgtaagagaag ... ttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG
          ttctgat  putative branch site (score: 44)
                                            ttttttttt  putative PPT
                                            ttttttttta  TA-rich tract