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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtactcaaatgatataatctggctgcttttgtttatgaatgtattgcctgaaaactctagtggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g73160.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G446960_T01 (Zea mays), 3'ss of exon 3
tgtactcaaat-gatataatctggctgcttttgtttatgaatgtattgcctgaaaactctagtggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG
  | || || |  |||||| |    |        ||     |      |  |||       ||| |  ||| | |  |  | | |||||||  | |||||| ||||| ||||| | ||| ||||||||||| ||||||||||| |||||||||||||| || || |||||||| ||||||||||| |||||||| || |||
-cttctaaattcaatataaacatcatatcacacattcctggttcgccactagaatctcactgtgaatccacggttgcttacatattctgtttatttggcagGGGCCCTCCTCGTTATGAAGGTGACAGGCCTAGGTTTGGTGATAGGGATGGTTACAGAGGAGGTCCACGTGGCGCTCCAGGTGACTTTGGTGGTGATAAG

upper sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171484_T01 (Zea mays), 3'ss of exon 3
tgtactcaaatgatataatctggctgcttttgtt-tatgaatgtattgcctgaaaactctag---tggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG
    ||   |  || || | | |    || | |  |||   || |||||  | | | | |     || || ||  | || |  ||| || ||||  | || ||| || || |||||||||| ||  ||||| || |||||||| || |||||||||||||| || || ||||| |||||    |||||||||||||| ||||||
---gcttctac-atttacttttgtacattatatcatattcctggattgctagtagagtttcaccatgaagccatggttacttacctattatgtttatttgacagGGGTCCCCCTCGCTTTGGGGAAGACAGACCTAGGTTTGGGGATAGGGATGGTTACAGAGGAGGTCCACGAGGTGCAATGGGTGATTTTGGTGGTGAGAAG

upper sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------------------tgtactcaa-atgatataatctggctgct-tttgtttatgaatgtattgcctgaaaactctagtggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG
                                                                                                 ||   | |  |  || | |  |||   || ||||  |    |||| |||  |   |  |||  ||  |  |      || |  |      |  |  |  ||| || || ||||||||||| || || || || |||||||||||| ||||||| ||| | || || ||||| ||  |||||||||| ||||||| | ||   
gtaatgactcaattttgagttgatgttcggtgatttatttatttatttatttatttattattctgttgttaaacaatttggtgcgcattggggttaatggtttgattacaatgtgaattgggatctgtttggattgccatgttttgtttttgagttcttatgatgtaaaatgggttttgttgaaaattgtgattttcagTGGTCCACCTCGCTTTGAAGGAGATAGACCAAGGTTTGGTGACCGGGATGGGTACCGTGGAGGTCCACGAGGACCTCCAGGTGAGTTTGGTGACAAGGGT

upper sequence: LOC_Os01g73160.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0050g01160.t01 (Vitis vinifera), 3'ss of exon 3
tgtactcaaatgatataatctggctgcttttgtttatgaatgtattgcctgaaaactct-agtggagacactgat-attatcctt--ttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG
        |||  ||||          |||| ||      ||  ||    ||    | | | | |  | | |||| | | |  |   || | ||    |   || ||||||||||||||||| || ||| | ||||||||||||||  | ||||| ||  | || ||||| |||||  ||||||| || |||||||| || |||
------gtaattctatatctctatcattttttttctatgttgggttcttagatttttttcacttggcatattgattaatgtgttaaattgtcttgagcttttagTGGCCCGCCTCGCTTTGATGGAGACCGTCCCAGGTTTGGTGATCGTGATGGGTATCGTGGAGGCCCTCGTGGCCCTCCAGGCGAGTTTGGTGGTGACAAG

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|16753351|gb|BM037730.1|BM037730
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGG-CCTCCTGGTGACCGCCCCAG                         AGGCCCACCTCGCTTCGAGGGTGACA-GCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88392465|gb|CI612939.1|CI612939
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88838789|gb|CI376327.1|CI376327
EST:     CCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: CCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88964009|gb|CI032926.1|CI032926
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|58611267|gb|CK038979.1|CK038979
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|25800605|gb|CA756566.1|CA756566
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88516474|gb|CI444128.1|CI444128
EST:     GCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: GCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|33660783|gb|CF291750.1|CF291750
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|33673990|gb|CF302229.1|CF302229
EST:     GGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: GGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|431819|gb|D23348.1|D23348
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|55435427|gb|CV730845.1|CV730845
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88353557|gb|CI632948.1|CI632948
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCG
EST: gi|66918916|gb|CX105764.1|CX105764
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCG-CCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|33670983|gb|CF299222.1|CF299222
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|86523561|gb|CI163767.1|CI163767
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88481347|gb|CI418618.1|CI418618
EST:     CTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: CTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|86599738|gb|CI255900.1|CI255900
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|33815880|gb|CF333787.1|CF333787
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|33659995|gb|CF290962.1|CF290962
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCC
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCC
EST: gi|58680699|gb|CK069386.1|CK069386
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGTGTGACAGGCCCAGGTTTGGTGA
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGG-GTGACAGGCCCAGGTTTGGTGA
EST: gi|33815878|gb|CF333786.1|CF333786
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
EST: gi|88329374|gb|CI653291.1|CI653291
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGC
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGC
EST: gi|55435537|gb|CV730899.1|CV730899
EST:     AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAG                         AGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG
genomic: AAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGG

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), 49 (downstream exon)
Score: 49

ACCTCAACCTGCCATCTGAGGTTGTGCCTAACACCCTCAAGAAGTCTGCCAAGCCCCCGTCTCGCCCATTCGGCTCTGGCCCTCCTGGTGACCGCCCCAGgtgagcattt ... cgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctgaaaactctagtggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG
                      cactgat  putative branch site (score: 49)
                              ttatccttttctgttc  CT-rich tract
                         tgatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtactcaaatgatataatctggctgcttttgtttatgaatgtattgcctgaaaactctagtggagacactgatattatccttttctgttcgtgtggcagAGGCCCGCCTCGCTTTGAGGGTGACAGGCCCAGGTTTGGTGACAGGGATGGTTACAGGGGTGGCCCACGTGGTGCTCCAGGTGATTTTGGTGGCGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- -actcaaa
- - - - - - - - - - - gctgctt
- - - - - - - - - - - - - - - - - -atgaatg
- - - - - - - - - - - - - - - - - - - - - - ttgcctg