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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcatttacctgttgtagcagcatagatgaacatcaatatctatattgatatttgtttagctcttgtagtttgatcattttttatgtcatattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT

Basic information

species Oryza sativa
transcript LOC_Os05g46580.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G079836_T01 (Zea mays), 3'ss of exon 1
gttagtgcattta--cctgttgtagcagcatagatgaacatcaatatctatattgatatttgt---ttagctcttgtagtttgatcattttttatgtcatattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT
||| ||| | |     || ||| || | | |  |  | ||||  |  | ||||| || ||| |   |||||| ||||  ||||||   | || || |  || | |||||||| || ||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||| |||| |||||| || ||||||||
gttggtgtagtgcattctattgcagtaacttgaactagcatccttg-ccatatttatttttttctcttagctattgtgatttgatagatgttaatttt-taatgtagATCGGCACCGACATTGAAGATTACAAGTGCTCATGGCTAGTTGTGCAAGCCCTTGATCGTGCTGATTAGAGCCAAAAGTGCATTCTATTT

upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 9
gttagtgcatttacctgttgtagcagcatagatgaacatc---aatatctatattgatatttgtttagctcttgtagtttgatcattttttatgtcatattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT
||| ||||||||| || ||  || | | |  |  | ||||       |   ||||  | ||   |||||| ||||  |||||||| | || || || || ||||||| || || ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||| || ||||||||
gttggtgcatttatctatttcagtaacttgaactagcatctttggcgtacttattttttttctcttagctattgtgatttgatcaatgttaatttc-taatatagATTGGAACGGACATTGAAGATTACAAGTGCTCATGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGCCAAAAGCGCATTCTATTT
















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|86427859|gb|CI072956.1|CI072956
EST:     TAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTGGGCTAGTTGTGCAAGCC
genomic: TAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|89168374|gb|CI109578.1|CI109578
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|58685683|gb|CK074370.1|CK074370
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|58685871|gb|CK074558.1|CK074558
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|58678948|gb|CK067635.1|CK067635
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|86434011|gb|CI094354.1|CI094354
EST:     AGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: AGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|88247621|gb|CI247470.1|CI247470
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|163928447|gb|EG711347.1|EG711347
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|88968869|gb|CI098954.1|CI098954
EST:     GACGATGATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
EST: gi|58674478|gb|CK063165.1|CK063165
EST:     GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAG                         ATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC
genomic: GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCC

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: 60 (upstream exon), 67 (downstream exon)
Score: 17

GACGATTATCTAGATTGTTATGGTGACCCCAAATTTATTGGCAAGgttagtgcat ... catattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgatatttgtttagctcttgtagtttgatcattttttatgtcatattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT
                           tttgatcattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcatttacctgttgtagcagcatagatgaacatcaatatctatattgatatttgtttagctcttgtagtttgatcattttttatgtcatattatagATCGGGACTGACATTGAAGATTACAAATGCTCTTGGCTAGTTGTGCAAGCCCTTGAGCGTGCTGATGAGAGTCAAAAGAGCGTTCTATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT