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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgacataaattttcattctttgtaccttcagatatttcttcagttttttttttcgtatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG

Basic information

species Oryza sativa
transcript LOC_Os06g44230.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G319000_T01 (Zea mays), 3'ss of exon 4
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||| ||||||||| || || ||| |  |||| |||||  ||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTATATTTCCGTGGGTGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G133353_T01 (Zea mays), 3'ss of exon 3
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtt------atgacact-----accacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||      || | |||     |    |||||||||||||||||| ||||||||||||||||||| ||||||||| || || ||| | |||||  |||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattactattcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttcattttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G475968_T01 (Zea mays), 3'ss of exon 7
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||| ||||||||| || || ||| | |||||| |||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTTTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G528717_T01 (Zea mays), 3'ss of exon 5
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||| ||||||||| || || ||| | ||||| ||||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G165454_T01 (Zea mays), 3'ss of exon 6
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              ||||||||| |||||||| ||| |||||||| ||||||||||||                                                                  
gtatgcagcataaataattactgttcattcttgctgagATACTGTGGTGCAGTTTATATGCTATTGCTTTGCTGGAATTATACTTGTTTCTTTTCTGTAAACATGTTGCTCGTAAATTGAGAGAGAAGGATGGATTTT------------------------------------------------------------------

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G467606_T01 (Zea mays), 3'ss of exon 5
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||| |||||||||||||| |||||||||| || || ||| | ||||| |||||  ||||||||| ||||||| | ||| | || |||||||
gtatgcagcataaataattactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAGTGAGAGAGGAGGATAGATTTTATTACCCTCACAATTTAGATTTCCGTGGGTGTGCATACCTTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G440258_T01 (Zea mays), 3'ss of exon 5
gtacgtgacataaattttcattctttgtaccttcagatatttctt----cagttttttttttcgtatgttatgacactaccac-----------ctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | | | ||  | | | | || ||  | |    |||||| | |  |  ||  || |   | |   ||           |||||||||||||||||  ||||||||||||||||||||||||||||| || || ||| | ||||| ||||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattactgttcattcttgctgagataccgtggtgcagtttatatgctattacattgttggaattatacttgttccttttctgtaaacagGTTGCTCATAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G370326_T01 (Zea mays), 3'ss of exon 7
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||  | ||| ||  | | | |  ||||| |    | |||||| | | ||  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||||||||||||| || || ||| | |||||  |||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataattattgttcattcttgctgagatactatggtgcagtttatatgttattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
gtacgtgacataaattttcattctttgtaccttc--agatatttc--ttcagttttttttttcgtatgtta-tgacactac----------cacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
||| |   |||||||    | | ||  | | | |  ||||| |    | |||||| | |  |  |   ||  ||  | ||              |||||||||||||||||| ||||||||||||||||||||||||||||| || || ||| | ||||| ||||| |||||||||||||||||| | ||| | || |||||||
gtatgcagcataaataaatactgttcattcttgctgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 3
---gtacgtgacataaatt---ttcattctttgtaccttcagatatttcttcagttttttttttcg-----tatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
      | | |  | || |   || |   ||   |  ||||    | ||    ||||   |  | |     ||  |||    |    ||    ||||||||| || || ||||||| ||| ||||| || ||||||||||| || ||||||||||| |||||  | ||||| ||||||||| | ||| | |  ||  |||
taatcgcataatctgaactaagtttaccattatcatgttcaatactatcccatgtttcactagttgagcaataatttaaagaaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCTCACAATCTTGATTTCCGTGGTAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 8
----gtacgtgacataaatt---ttcattctttgtaccttcagatat-ttcttcagttttttttttcgtatgttatgacactaccacctgt---aaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
     | | | |  | || |   ||   | |   ||  |||| || | |||   | ||   |   |   |  | ||  || ||  |    |   |||||||| |||| |||||||| ||| ||||| || |||||||||||||| ||| |||| || || ||| | ||||| || |||||| | ||| | |  ||  || 
agtgttgcataatctcaactaaattttgtataattattttcaaatctattccataattcactaactgaaaattaattgcaataaaatacatttgaaacagGTGGCTCAGAAAATGAAAGATGAGGAAGGCTTTTATTATCCCCACAATGTTGACTTCCGCGGCAGAGCATATCCCATGCATTCTCATTTGAATCATTTAA

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
---gtacgtgacataaatt---ttcattctttgtaccttcagatatttcttcagttttttttttcg-----tatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
    |   | |  | || |   || |   ||   || ||||    | ||    ||||   |  | |     ||  |||    |    ||    ||||||||| || || ||||||| ||| ||||| || ||||||||||| || |||||||| || |||||| | ||||| ||||||||| | ||| | |  ||  |||
taattgaataatctgaactaagtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG

upper sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtacgtgac-ataaattttcattctttgtaccttcagata--tttcttcagttttttttttcgtatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
             |  |||  ||  |||  |||   | | |   ||  | |  ||| |||| || |    |||   || ||   ||    ||  | | ||||||| ||||| ||||||| ||| || || || ||||||||||| || |||||||||||||| |||||||| ||||| |||||| ||||| | |  || ||  
tttcctaatgcagatttgattatgtattgccatgactggaagtctcgaagaactttgttcatttgtaagcttca-gtgcta-agcagattcattt-tgaacagGTGGCTCGAAAAATGAAAGATGAAGAAGGCTTTTATTATCCTCACAATCTTGATTTTCGAGGCCGTGCGTACCCAATGCATCCACATTTGAATCATCTGA

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: 12

TCCAGATGAAATACAGAAATGGAAGTGGAGCTTAAAGAAGGCAAAGAAAGCTAATCGTGAACTGCATGCTGAGCGATGCGATACAGAGCTTAAACTATCTgtacgtgaca ... ctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatttcttcagttttttttttcgtatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
         ttcagtttttttttt  TA-rich tract