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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctctacaaacaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g05340.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G155384_T02 (Zea mays), 5'ss of exon 13
TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctctacaaacaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag
||| |||||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || |||||||| ||||| |||||||||| |  | ||||    |||||   | |  |||  ||  | ||  | | | |    |     |  | |||||||
TTTGATTGATGGTCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTGGCCAGgttagcttttgagacaac-ccttactagcaatgttttt-gaaaagagtttaagtttttttat----tgctttgtgcag

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 5
TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctctacaaacaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccatatc----ttctgtgcag
||| |||||||| |||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| || |||||||| |||||  ||||||||| |  | |||    ||||||      | |||  || |||||| |  || | ||   | | |      | |||||||
TTTGATTGATGGCCGTGGTGCCAGCTCCAGTCTTGATTCCGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTGGCAAGgttagcttttgagaca----gttact----aatgtttgtgaagaaagacttcattttaacttctttttattactttgtgcag

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
-TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgt-------tagctctacaaacaatatgttacttttagt-tctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag-----------------------
  || || |  |||| | ||||  |  | ||| ||||||| || ||||| ||  | |||||||| ||||| |||||||| ||||||||||| |||||||||||       ||  |  | |  | |||||||   |||  | |  ||  | |  ||  ||   |   |   |   |||||||                             
GCTTGATGGCCGGGC-TAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 13
-TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgt-------tagctctaca--aacaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccat--atcttctgtgcag-----------------------
  || || |  |||| | ||||  |  | ||| |||| || || ||||| ||  | |||||||| ||||| |||||||| ||||||||||| |||||||||||       ||  |||| |  |  ||| |  || || | ||  |||  |   || ||   | |||      | |  |||||||                             
GCTTGATGGCCGGGC-TAGTGCTGGTGCAAGTGTTGACTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttctagattatgaatgttgtatttgttgtgattttgggttaatgatctattcttctattcctcaatcttctacttctcacttcccattatcattgtgcag

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 11
-TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgt-tagctctacaa-acaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag
  |  |  |  |||| | |  || |  | ||  | |||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| ||||||||||| | | |  | |  | ||||   ||  | ||||         ||||    ||       |    || |  |    ||||
ACTCGACGGCAGGGC-TAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTTTTGGTCAGgtatggttgcagattataataaaatagatctagt---------ggaagacgtgtcctcttaatatatttgcttatcgcag

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|29667414|gb|CB663689.1|CB663689
EST:     ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
EST: gi|86823672|gb|CI258732.1|CI258732
EST:     ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
EST: gi|58604809|gb|CK015337.1|CK015337
EST:     GGATTTGGTCAG                         GATAAGTCGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: GGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
EST: gi|58685643|gb|CK074330.1|CK074330
EST:     GCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGATAGCGGAGCTTCTGG
genomic: GCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAG-TAGCGGAGCTTCTGG
EST: gi|58605592|gb|CK033625.1|CK033625
EST:     ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
EST: gi|29634005|gb|CB639014.1|CB639014
EST:     ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: ATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
EST: gi|58681049|gb|CK069736.1|CK069736
EST:     GCTGGATTTGGTCAG                         GATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA
genomic: GCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGA

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), 71 (downstream exon)
Score: 40

TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctcta ... ttctgtgcagGATAAGTTGATGACTGCTCCATCTGATTCTTCCAGTAGCGGAGCTTCTGGAAACTGGTTATTCAAGAACAAGGAACATGGGAAAGCCAGCGCAGCAGCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgttagctctacaaacaatatgttacttttagttctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA