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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
gtttgttatcttaagttatgct-ttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
||||||  | || ||||||| | |||     | ||| || ||           | || |||| ||| | |  ||| ||||||||||||||||||||||||||| |||||||| ||||||||  | |||||||||||||||||||| ||||| ||||| || || |||||||| |||||||
gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttc--------ttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 16
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaa----cagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
|||||  || | ||||   |||    || |||  | |   ||     ||   |  | ||||   | ||| |    |    ||||| || |||||||||||||| || ||||||| ||| |||||  | ||||||||||| || ||| | |||||||| || || || || ||||||||  |||
gtttga-atttcaagt---gctaaagtgactggatctatctaaaaattg---ttatttattcttatcatgaaatgattttcagGCTCTAGTTGAGTTCTTTGGAACCCTTTCAAAAGAATGGGCGCTAGAGTGCATGAAAGATCTTTTACTGGTCAACCTTAGGGGCAACCTTCAAATAATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 18
gtttgttatcttaagtta--tgctttgttgcctg--tctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
          || | | |  ||||    || |||  |||||    | |   |    |  |||  | |    || |||   ||||| || |||||||||||||| |||||||||| ||| |||||  | ||||||||||| || ||| | |||||||| || || || || ||||||||  |||
--------gtttgaatcaagtgctaaagtgactggatctatctaaatttttttatttattcttatcatgaaatgatttt-cagGCTCTAGTTGAGTTCTTTGGAACTCTTTCAAAAGAATGGGCGCTAGAGTGCATGAAAGATCTTTTACTGGTCAACCTTAGGGGCAACCTTCAAATAATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 17
gtttgttatcttaagttatgctttgttgcctgtctattattac----tggctggggtggtctatttacaccattattgaa------cagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
||||||  | ||   ||    ||| |    | |||||| | ||    ||   |   |    || |||   |||| ||         ||| |||| ||||| || ||||| ||||| ||| |||| ||||| || ||||||||||| || ||  ||||||||||||| ||||| || || || ||| |||
gtttgt-gtgttccattgc-ttttataatttatctattgtaacatcatgctagttttaaaatactta-gtcattgttcggttcttgcagTCACTCGTTGAATTTTTTGGTACTCTGTCACGAGAATGGGCATTAGAGTGCATGAAAGATCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 17
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtcta---tttacaccattattgaa------cagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
||||||  |  |   ||    ||| |    | |||||| | ||    ||      | ||   | |    |||| || ||      ||| |||| ||||| || ||||| ||||| |||||||| ||||| || ||||| ||||| |||||  ||||||||||||| ||||| || || || ||| |||
gtttgt-gtgatccattgc-ttttataatttatctattgtaacattatgctagtttttaaattcttagtcattgttcaattcttgcagTCACTCGTTGAATTTTTTGGTACTCTGTCAAGAGAATGGGCATTAGAGTGTATGAAAGACCTATTGCTGGTCAATCTTAGAGGCAACCTACAGATTATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 18
--------gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggt-----------ctatttacaccattattga-acagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
        | |  |   |||    | |  |||  ||  |  | ||||  ||    || |   |            ||| | |     |  |||  |||| ||||||| ||||| ||||| || || |||| ||| ||||| || ||||||||||| ||| | ||||||| |||||| || || || || || ||  |||
gtttatgtgctgttctgcttttaatctattttagtgtttaacaattaaaacccattgtgtgagcttttaaaatacctactcattatgtggttgttacagTCACTTGTAGAGTTTTTTGGTACACTGTCAAAAGAATGGGCATTAGAGTGCATGAAAGACTTACTGCTGGCCAATCTTAGGGGCAACCTACAGATCATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 18
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctat-ttacaccatt--attgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
|| |    ||| || | ||  || |||||    | | |     ||     | || |  || |  | | | |  | |   ||||| ||||| ||||| ||||| |||||||| || ||||||||  ||||||||||||| || || ||| ||||||| || ||||| || ||||| ||  | |
gtattacctctgaactaattgttggttgctaaacaact--cgatgttcaagttgctgaatatccctctactcaaatttgcagGCTCTTGTCGAGTTTTTTGGTACTCTTTCTAGCGAGTGGGCAATGGAGTGCATGAAAGATCTCCTGTTGGTCAACCTGAGAGGCAACCTTCAGATAATCG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatt-tacaccattat-tgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
  | ||     | |  |||  |||| |   |     |  | | |||    | || |  ||   || |   |   |   ||||| ||||||||||| |||||||||||||| || ||||||||| |||||||||||||||| ||  |||||||||| || ||||| ||||| || ||  |||
-gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 18
gtttgttatcttaagttatgctttgttgcctgt-ctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
||| | |     ||||   | |   |  | ||| |||||   |     |    |  ||||  || |   | ||    ||||| ||||||||||||||||| |||||||||||||| |||||| | ||||| ||||| |||||||| || ||||||||  | |  |||||||| ||  |||
gttagatgctcaaagt---gttacataacttgttctatttgaatgtagtatttttttctaactatatggt-atatttcagGCTCTTGTTGAGTTCTTTGGAACTCTTTCAAGAGAATGGGCTCTTGAGTGTATGAAAGACCTTCTACTTGTCAATCTTCGTGCCAATCTTCAGATAATTG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
|||| |   ||| |  | || ||  | |            |  |      | |  |  ||         | ||   ||||||||||| ||||||||||| || |||||| |||| ||||||||||||||||||||||||||||| ||||||||||||||||| || ||||| ||  |||
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctctt---cagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG

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: 63 (upstream exon), 75 (downstream exon)
Score: 89

CATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAGgtttgttatc ... tattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG
        tctattatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttatcttaagttatgctttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG