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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA

Basic information

species Oryza sativa
transcript LOC_Os08g33830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 1
--------ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
         ||   | || ||  ||| |  |  | | |    |    |        | | |   ||||| ||      || || |    | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||| || |||||||
actgtatgctgcacttgcagagtttttagttctatatta---ttcgaatctcctgcttagtcagtgttcctta-----cagttgtcccttcaacatgcacattttcagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGCGGTAAAACTGTCTATATCCAATATTCAAACA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 1
----ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA----
     |||  | || ||  ||| |  |    | |    |    | |      | | |   ||||||||  |  |  |        | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || |||||||    
tatgctgaacttgcagaccttttagttttgtatta---ttcgaatttcctgcttagtcaatgttctttactgttttccct-----tcaacatgctcattttcaggcagATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACAGGCA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082174_T02 (Zea mays), 3'ss of exon 1
--------ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
         |||  | || ||  ||| |  |    | |    |    | |      | | |   ||||||||  |  |  |        | ||  | |   |||||||||||||||||||||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| || |||||||
actatatgctgaacttgcagaccttttagttttgtatta---ttcgaatttcctgcttagtcaatgttctttactgttttccct-----tcaacatgctcattttcagGCAGATCAAAACCAGGCAATTTCAATGGTGTCCTATTATGCTTCATCTTCAGAACCTGCTCAAGTTCGTGGTAAAACTGTATATATCCAATATTCAAACA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 1
-ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtacctttttt--cagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA-
  ||| | |     ||| ||  | ||   ||   || || | |  |   |     |   || |||  |  |   |||  |   || | ||| |  |||  ||||  |||| ||| || || ||||| |||||||||||||||||||| ||||||||||| |||   |||||||| |||||||| || || ||||| || || | 
agtgactgatt---agtgtctgaggatgtgttttct-tatatttaatgatacccggtcctttttttatgattttttaactctcaagtatacatgctttaccaggTGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATAG

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 1
ttgatttagcggaagtttcaa-atgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
 ||| |   ||   ||   |  |||     |    | |    ||     ||  |   | || ||| ||  |   |||  | |   ||  |   |||  ||||| |||| ||| || || ||||| |||||||||||||||||||| ||||||||||| |||   |||||||| |||||||| || || ||||| || || |
gtgact-gccgagcgtccgaggatgtgttttcttatatttgatgatacctggttctttttttttttttttttttttaactcaattatacatgctttgccagGCGGATCTAAATCAAGCCATTTCGATGGTTTCATATTATGCTTCATCTTCAGAACCAGCTATGGTTCGTGGTAAAACTGTTTACATTCAGTATTCTAATA

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 1
ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctt-tgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
   ||  |   |   | |||| |         |   | |      | |  |  |   ||| |   | |    | | ||     |    |    |||| ||||| ||    || || || || ||||||||||| ||||||||||| |||||||| || || ||  ||||||| |||||||| ||||| |||||||| ||  
-gtatcgaataggtttctcaagttttatagctatgatggttgactcttcaagctttcgttttggcgatttctattgatgaaccattcatttgattttacagGCTGACTTGAATCAAGCTATATCAATGGTTTCGTATTATGCTTCATCTTCAGAGCCCGCACAGATTCGTGGGAAAACTGTCTATATTCAGTACTCTAATC

upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 1
--ttgatttag--cggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
   ||| || |  | |   | | ||||  |    ||  || ||  |   | ||   |   || |  | | |     || | |  | |  | ||  | ||| |||   || |  || ||||| ||||| |||||||||||||||||||| ||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||
tggtgacttggatccgggttattaaatttatttcgagatgcagtttt--ctttttctctttggtggtggctatatgctgaca--aaaggtatatttctttgcagTTGGACCTTAATCAGGCCATTTCTATGGTTTCATATTATGCTTCATCTTCGGAACCTGCACAGGTTCGTGGTAAGACTGTGTATATCCAATACTCTAACA

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|58612262|gb|CK039974.1|CK039974
EST:     GCCAACCGCAACCAGGCCTTCGTCGAGTTC                         GCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
genomic: GCCAACCGCAACCAGGCCTTCGTCGAGTTCgtaaggacac ... cttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
EST: gi|58609701|gb|CK037734.1|CK037734
EST:     ACACCATGTGCAACGTCGGCGCCAACCGCAACCAGGCCTTCGTCGAGTTC                         GCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
genomic: ACACCATGTGCAACGTCGGCGCCAACCGCAACCAGGCCTTCGTCGAGTTCgtaaggacac ... cttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
EST: gi|66921961|gb|CX108809.1|CX108809
EST:     ACCGCAA-CAGGCCTTCGTCGAGTTC                         GCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
genomic: ACCGCAACCAGGCCTTCGTCGAGTTCgtaaggacac ... cttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
EST: gi|58688477|gb|CK077164.1|CK077164
EST:     ACACCATGTGCAACGTCGGCGCCAACCGCAACCAGGCCTTCGTCGAGTTC                         GCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA
genomic: ACACCATGTGCAACGTCGGCGCCAACCGCAACCAGGCCTTCGTCGAGTTCgtaaggacac ... cttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCA

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), 72 (downstream exon)
Score: 24

CACCGAGGAGGAGCTCGTCGAGCTCTGCAAGCCCTTCGGCAGGGTCGTCAACACCATGTGCAACGTCGGCGCCAACCGCAACCAGGCCTTCGTCGAGTTCgtaaggacac ... cttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA
                     tcctcac  putative branch site (score: 24)
                                          taccttttttc  putative PPT
                            ttatattataaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatttagcggaagtttcaaatgaacagtgaactgtagactggacattgaattgctgttctttgttcctcacttatattataaatgtaccttttttcagGCAGATCAAAACCAGGCAATTTCAATGGTTTCATATTATGCTTCTTCTTCAGAACCTGCTCAAGTTCGTGGCAAAACTGTATATATCCAGTACTCAAACA

- - - - - - - - - - -atgaaca
- - - - - - - - - - - - - - -tgaactg
- - - - - - - - - - - - - - - - - - - - ctggaca
- - - - - - - - - - - - - - - - - - - - - - - - - -attgctg