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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG

Basic information

species Oryza sativa
transcript LOC_Os10g40550.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
--gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCT---GATTCGAGTGGTCAGCATG
   ||  |  ||  ||||||  || | || |   | |||   | | ||||||||||||  ||| |||||                       |  |||||||||||||||||||||| |||| |||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||| ||   || || | |||   |    
gtatacagtgttattgttcat-tgcacaa-ataactcctatcagcattttgcattttt--ctcattgtt-----------------------tcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG---

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G00790.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                       | |   || |  |  | ||  | | | |||||  ||   ||     | | || |    |  | |||    || ||  || |     |  |   | |||| | | | |||||   |||||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||  | ||||  ||   |  ||| |   
gtagttgaacaatttttataaaaaacagacaattttctatctctttttaattcccttatctatctgagcac-cacttcatacactcctgctttcaagaagcttccttgtcggttgctcgttctaactttcgaat-tacccctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTCTATTATGCTGGTAGTCATGGAATGGACATCATTGGGCCTGTTAGACAATCTGTATCTGATAATCACCCAA

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
-------------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                        | |   || |  |  |   || | |  |||||  || | ||     | | || |    |  | |||    || || |||    | | | |   | |||| | | | |||||   |||||| ||||| ||||||||||| |||||||||||||| ||||| || ||||||||  | ||||  ||   |  ||| |   
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcata-cactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgt-tggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S46_31V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcact-ctttgttgactctctcttatgtgtgttttgttctt----tagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
    |||  ||  |      |||   |   |      | |        | | ||    || |  |   ||     |||| ||  || || | | ||     |||| ||||| |||||| || | || ||||| |||||||||||||||||||| |||||||||||||| ||||  | ||  || |||  |  | |   | | |
---tggatcttcagaaattttgtgcgaagttgatttaggtttgtgaagggagttgaagctacaattaagaggtcttcttgtggttgcttcgattttggagcagGTGTTTGAGTTTGTGCAATTGACAGAACTATATTACGCTGGAAGTCATGGCATGGATATCATGGGACCTGCAAAGAGTTCAGATGGGTATCGAGTGAAGG

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S333_42V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------gtaaggaatttatgttcacatgta-----aaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                                                                                                     |  |  | |||    |   |||||     ||||       | |  |    | ||| | ||    ||  ||| | ||     |  | ||| ||| |  |   |||| |  || || ||| || || | ||| | ||||||||||| |||||||| ||||| |||||||||||||  |     || |||     | ||  | | |
gtactgacaggattcctggtattctgattctgtatcacactctgtccttgagcattggcttgtttctgttaaatccatacattgattcacatgaccttgatgcgaatattttgcagttggatgtagtgtcaaatcaaaattccgagagggatatgc-tgttgggatcgctgt-gcctacagttggtatgtttttggagc---agGTGTACGATTTCGTGCAATTATCAGAATTATATTACGCTGGGAGTCATGGTATGGACATCATGGGGCCTGCGAATGGCTCCGATGGTTTTCGTGTGAAAG

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S141_116V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------gtaaggaatttatgttcacatgtaaaatactccccc----tgctaaccttttgcatttttcactctt-tgttgactctctct-------tatgtgtgttttgttcttt--------agGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
                                                    | ||    |     ||  |  | || |  |||  |    || ||   ||||   |||||   | |  |  ||| ||   |        | || | || ||  ||| |        |||| |  || |||||| ||||  | ||| |||| ||||| |||||||||||||||||||| ||||| ||||  |  |  ||   || ||  |   |||| |   
gtgaggcttcggtcgttcttttcatagcagtttcctcggtcatggaaaatatttagtgggtggccatcgtacttcaattcttccttcgcattggtacatttttaattttttttttatcatagtgattcatgccaactgaatgtgggcgtattactctatttttgaacagGTATACGATTTTGTGCAACTGTCGGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAA-AGTCAACG--

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S227_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgtt--gactctctcttatgtgtgttttgttctt----tagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
     | || ||| || | || | ||  |       |  |       |||||     |   |   ||  ||  |   || |    | || || | ||     |||| ||||| |||||| || | || ||||||||||||||||| |||||||| |||||||||||||| |||| ||  |  ||   || ||   | | | ||    
----tggatctattttgagattttaatcaggattgattttggtgagatgcatgcgaaagcttcaattaggaggcgtgctcacagcttttatggttttggagcagGTGTTTGATTTTGTGCAATTGACAGAACTGTATTACGCTGGGAGTCATGGCATGGATATCATGGGCCCTGCTAAAAGCTCGGATGGTTTCCGAGTTAAGG---

upper sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtaaggaattta--tgttcacatgtaaaatactccccctgctaacctt-ttgcatttttcactctttgttgactctctct---tatgtgtgttttgttcttt--------agGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTC---TGATTCGAGTGGTCAGCATG
                                                               ||||   || |  | ||| |  | |   | || |   |  |    || ||   |||||   | |||| |||   |  |    |||  |||  ||||||  |        ||||||  || |||||| || |  | ||  |||| || ||||||||||||||||||||||| ||||| ||||  |  |  ||   || ||  |   |||| |   
gtgagtctttggtccgtcgtttctctatgtagtcgaaaacgttgtgtggatgaccattgtacttaagtctttcaattattctcg-gcattttgcttcgttttttttttttcttttttttttttttttttgctgaacataacccaatatcggtgaattgttcgattctgaaacagGTTTACGATTTTGTGCAATTGTCGGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGCAAAAAGTTCAAGTGGTTTTAA-AGTCAACG--

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: 48 (upstream exon), 57 (downstream exon)
Score: 11

ATGCGCTCTGCTGTGAAGCATGTGGCATCACTTTTTCCCACTGCGATCATTAGTGGAAGATCTCGTGATAAGgtaaggaatt ... tgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCTGATTCGAGTGGTCAGCATG
                    tgttgac  putative branch site (score: 11)
                                          ttttgttcttt  putative PPT
       atttttca  TA-rich tract