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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctctatctctatgtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT

Basic information

species Oryza sativa
transcript 13113.m00246
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 16
--gtaaatctctatctctatgtgtgcatgcacac-gtctggtgctgaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
   |  | ||||   | | |  ||     ||| | ||||  | || |      | || ||||   ||| | |  |||||||||||||||||| |||||||||||||| ||||||||||||||||| || || |||||||| ||| | |||||||||||||| ||| |
gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttatttttaactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
gtaaatctctat-ctctatgtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
|||     || | || | | |  ||      || | | || || |   |||||| |||||   ||| | |  |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||| | |||||||||||||| ||| |
gtatgctcctcttctatttttaggccatggtac-tgtagtacttat-ttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 16
-------------gtaaatctctatctctatgtgtgca----tgcacacgtctggtgctgaaactgacctaat-tttgtttg----------ttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
              | | ||| |||||  |  | |  |    |   ||| || | ||   |   |  | || | ||| ||||          | ||||||| ||||| |||||||||||||| |||||| || | ||||||||||  ||| | ||||| |  || || || ||||| || ||||| ||  |
gtaaacattggccttcattctgtatcttgagttattgaatttttttcac-tccgatgtatatttttgcttattgtttttttgggggggattctgactctagTTACTCGGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGCCCTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 16
-------------------------------------------------------gtaaatctctatct-ctatgtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
                                                       ||| || | |   |  ||| | |  ||  |    | |  |  |      |          | || | ||||||| ||||| |||||||||||||| |||||| || | ||||||||||  | | | ||||| |  || || || ||||| || ||||| ||  |
gtaaacattggccttcattctgtatcttgagttattgaaattttcctgctctgatgtatatttttgcttattatttatttatttatttattt--tttttggggggggggggggggggttctgactctagTTACTCAGAGTCTGAATACTTCAAGCAAACAATGCGCCAAGGTGGTCTTACTAAACCAAAAGAGCCTCGTATTCCTAGGATGCCTCAATT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
--------------------gtaaatc-tctatctctatgtgtgca-tgcacacgtctggtgctgaaactgacctaattttgtttgtta---ctctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
                     || ||  |  |   |||| |   || |   ||  |||       | |      |  |||| | |  |    ||  ||||||||||| ||||| |||||||||||| || | || |||||||| || || |||||||  || ||  |||||||  | ||||| ||  |
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatcccttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 16
------gtaaatctctatct------ctatgtgtgcatgcacacgtctggtgctgaaact---gacctaattttgtttgttactc-------tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
      || ||| |  |  |       ||||| |  |     | || |     |   | |   ||| |  ||   |||  |  ||       ||| ||||| ||||||||||||||||||||| || | || |||||||| || |||||||  || || ||  |||| ||  | ||||| || ||
gtaattgtgaattttcagttgccaacttatgt-tataattttatgtttttcattatcatttaagacatgtttccattttcttgtcctttaagtagTTACTCAGAGTCTGAATACTTTAAGCAAACAATGCGGCAAGGTGCTCCAGCAAAACAAAGAGAGCCTAGAATACCGCGCATGCCCCAGCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58673121|gb|CK061807.1|CK061807
EST:     CTGGTCAGTGAT-ACTGGATAGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGC
genomic: CTGGTCAGTGATAACTGGATAGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtaaatctct ... gttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGC




















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: 74 (upstream exon), 62 (downstream exon)
Score: 53

TTTACATTCTTGATTTCTTGAAGGAGGAAAACAAGCTTGATTTTAAGAAACTGGTCAGTGATAACTGGATAGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtaaatctct ... gttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactctagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT
                                              ttactct  CT-rich tract
                                  taattttgtttgtta  TA-rich tract