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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA

Basic information

species Oryza sativa
transcript LOC_Os06g50300.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G141931_T01 (Zea mays), 3'ss of exon 7
------attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
            ||||||  ||| | | | || | |   | |  | |||||      |    |       | || |  |||  ||||   ||||    |  ||||||||||||||||||||||||||||||||||||| ||||| || || |||||| | ||||||||||||||||| ||||||||| |||||||||||||| |||
gtctgctccaccctgcatc-tcttgtagactt-tataagacaagt-ctatttgtttgtgcatctgttgttacaagtgtctaatttga---tttctcttttatgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAACTTCCCTATCTATTTGTGGTCGACCAAGGAGGTTGATGTTGAAGTGCCAACTGATGAGGATGAGACAA

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 7
attttgctg--catagt---ctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
 ||  ||||  |||| |   |||  | |  ||| ||  ||||    ||||    |||  |         | || |   ||  | ||||   |||   |  || |||||||||| ||||||||||||||||||||||| ||||| || || |||||| ||||||||||||||||||| |||||||||||||||||||||||| |||
-ttgggctggacatattatactgaaacacatctcttatatagaccttatttgtgcatc-tgttgttgttacaagtgtttaattcgaac---tcacttttatgtagGATTTGGTTAAGAAGTACTCTGAGTTCATCAACTTCCCTATCTATTTGTGGTCAACCAAGGAGGTTGATGTTGAAGTGCCAGCTGATGAGGATGAGACAA

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaa-taacttactatc-ttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
||    ||   |       |   ||| |||  |||| || || |  | |    | ||    |    |  || | |||  || ||||  |  |  | |  ||||| ||||||||||  |||||||| || || || ||||| || ||  | ||||||| ||| |||||||||||||| || || |||||||| ||||| ||  
ataaaactcatttaatatacgtttttttgtc-aatatctactctcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 7
------attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
       |||||||   || | |  ||| |   | | | |    |  | |   |  | |||       |  |   ||   || |||     || ||  |  || |||| || ||||| |  || ||||| |||||||| || ||||| ||| | ||||||| ||| ||||||||||| || || || || ||||| ||||||||||
agttaatttttgctttttatttttccaa-tgaatatgggagcattcttgtgatgtaaatatctggtttaggt---ttttaattttgctaccttgataat--tgtagGAGTTAGTGAAAAGATATTCTGAATTCATCAACTTTCCCATATACCTCTGGGCAAGCAAAGAGGTTGATGTAGAGGTACCTGCAGATGAAGATGAGTCAA

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 7
attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataactt-actatcttgaacatttcatggtct---tgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
    ||     || |   | || |  || |      |         | | |     ||  |    ||| || ||  |||    |  || ||  | |   |||||||  | ||||||||||| ||||| |||||||  ||||| |||||| ||||||| | ||| ||||||||||| |||||||| | ||| ||||  ||    |
----tgacttttaattgaggaagtaactttctggaggtaagggactaaataggtggcagtgtttttaattttacagtctaattctgttgataatttgagtgcagGAACTCGTGAAGAAGTATTCTGAATTCATCAGCTTCCCTATTTACCTGTGGGCTAGCAAAGAGGTTGATGTTGAAGTGCCCGTTGAAGAGGCCGAAGAGA

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|570127|gb|D40976.1|D40976
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
EST: gi|29635203|gb|CB640212.1|CB640212
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
EST: gi|5803546|gb|AI978516.1|AI978516
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
EST: gi|29622518|gb|CB627529.1|CB627529
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTAC
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTAC
EST: gi|569681|gb|D40530.1|D40530
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
EST: gi|571725|gb|D41236.1|D41236
EST:     TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAG                         GATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG
genomic: TGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGG

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), 74 (downstream exon)
Score: 163

CTCTGAGGATACATGGAATGAACCCCTGGGCCGTGGAACTGAAATAAGACTGCACCTCCGAGATGAAGCCAAGGAGTACGTGGAAGAAGACAAGCTAAAGgtattaccat ... ggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA
                     aacttac  putative branch site (score: 163)
     attatacaaagaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgctgcatagtctggcaaatttctgttgaatagctgctattgagacattatacaaagaaaataacttactatcttgaacatttcatggtcttgcagGATTTGGTGAAGAAGTACTCTGAGTTCATCAATTTCCCCATTTACTTGTGGGCAACCAAGGAGGTTGATGTGGAAGTGCCAGCTGATGAGGATGAGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - tgctgca
- - - - - - - - - - - - - ctgttga
- - - - - - - - - - - - - - - - - - gctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa