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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaggacttgttttactctaataatactatctttaccacttaaggatttctaactacaagcccttctcaatgttaaataataataataagaacaactcttaatgtttgctaaactcgagtaactaaaatgacatgtctttgatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG

Basic information

species Oryza sativa
transcript LOC_Os12g18110.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g18110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 7
gtgagca--ggacttgttttactctaataatactatctttaccacttaaggatttctaactacaagcccttctcaatgttaaataataataataagaacaactcttaatgtttgctaaactcgagtaactaaaatgacatgtctttgatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG
|||||||  | |    |      | |  ||||   |||||| |          || | || ||    | || ||  ||               |  ||  |||| |  || ||||  |||         ||||||    | |||||| | || |||||    |||||||| ||  || | ||||| ||||||||||| ||| |||||||||||||    || |||||||||||||| |||||||||||||||||||
gtgagcacagcatccatccagtgccagcaatatattctttatc----------ttttgacaacgcatcgttatctgtgc--------------agaaattactcatgctgcttgcagaac-------gttaaaata--ttctctttgtttttttagGAGACGGTTTTCTTTGATGTCCTGTTCATTATCCAACACTACGTGTTGTACCCTGTCAAGAAGGACGAGAATGGTAAGGCAATCATTTCTGAAAGGGTAG
















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|89191255|gb|CI393108.1|CI393108
EST:     AAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: AAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|88275408|gb|CI395259.1|CI395259
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|88289221|gb|CI553197.1|CI553197
EST:     CTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: CTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|38482937|gb|CF966739.1|CF966739
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|86887884|gb|CI297995.1|CI297995
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTG
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTG
EST: gi|88829632|gb|CI074502.1|CI074502
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACGCTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|86865764|gb|CI335454.1|CI335454
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|88515837|gb|CI443491.1|CI443491
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|86833032|gb|CI333631.1|CI333631
EST:     ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
EST: gi|88564376|gb|CI495093.1|CI495093
EST:     GGAAATATTGGGAAAACCCTTCTTTCATTG                         GAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC
genomic: GGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTAC

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), 72 (downstream exon)
Score: 32

ACACGCTAGTGAACTTCTATGGAAATATTGGGAAAACCCTTCTTTCATTGgtgagcagga ... gatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttaatgtttgctaaactcgagtaactaaaatgacatgtctttgatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG
                        taactaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaggacttgttttactctaataatactatctttaccacttaaggatttctaactacaagcccttctcaatgttaaataataataataagaacaactcttaatgtttgctaaactcgagtaactaaaatgacatgtctttgatattgtagGAAGTCGTTTTCTTCGACATCTTATTCATAATCCAACACTATGTGCTGTACCCTGTCAAACGAGATGAGAATGGTAAGGCTATCATTTCTGAAAGGGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG