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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacattaacatatgagccccttcctttatggcaataggagaaaatgaagcagcttctctaataatgctcttccaattatgttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G840582_T03 (Zea mays), 3'ss of exon 11
gtgacattaacatatgagccccttcctttatggcaatagg-agaaaatgaagcagcttctctaataatgctcttccaattatgttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT
              | |||  |    ||| ||    |  | ||  |||  ||     | | |  |  ||     |   || ||||| ||||||||||||||||||||||||||||||||   | ||| ||| ||| || || || || || || || |||||||| || || ||||||||||||||||||||
-------------gtaagcatcaagatttctgttggtttgcagcgaatagagtgtggtttatttttgtga----ctggttgtgttgctgcagGAGCTATGTACTCTTTCCCCCAAATACAGCTGCCAGCAAGAGCCATCGAGGCGGCAAAGAGAGCCGGCAAAGCAGCAGACGTTTTCTACTGCCTCAAGCT

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 12
-------gtgacattaac--atatgagccccttcctttatggcaataggagaaaatgaagcagcttctctaataatgctcttccaattatg----ttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT
        |  |  |  |  | || |     |   || |||  | | |    |  |        |  |  ||   || |     ||| |      | ||| |||| || |||||||| ||||| ||||| || || |||||||||||||| || || ||||||| |||||| |||| ||| |||||||||||||||||||||||
gtaaaaaattgctcttccgaagattacattttattttcatgcaatttgtgagacgttttttcaatatttaaaagttggttgattaatgagaaaaatggtttcagGGGCCATGTACTCATTCCCTCAAATTCGATTGCCACCAAAAGCTATTGAGGCTGCCAAAAAGGCTGGTAAAGTGGCTGATGTTTTCTACTGCCTCAAGCT
















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|29671704|gb|CB667979.1|CB667979
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCC
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCC
EST: gi|29645692|gb|CB650699.1|CB650699
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTC
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTC
EST: gi|29615822|gb|CB620834.1|CB620834
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|33801487|gb|CF326616.1|CF326616
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|33381971|gb|CF197314.1|CF197314
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|5667553|gb|AU077813.1|AU077813
EST:     GACAGATGGTTTCANTAGNTGCCGAAATGTTGTCTGCAATTTCACANNAG                         GAGCTATGT-CTCTTTCCCCCAAATACGCTTACCACCAAAAGCTCTAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|33381462|gb|CF196805.1|CF196805
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|11442608|gb|BF430511.1|BF430511
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
EST: gi|38479882|gb|CF963971.1|CF963971
EST:     GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAG                         GAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG
genomic: GACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATG

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: 72 (upstream exon), 72 (downstream exon)
Score: 124

CAAGTCTATCCTCGAGTCTTTGAGGAGGAGAGCACGCCTGATGACAGATGGTTTCAATAGTTGCCGAAATGTTGTCTGCAATTTCACAGAAGgtgacattaa ... gttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggagaaaatgaagcagcttctctaataatgctcttccaattatgttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT
                     ctctaat  putative branch site (score: 124)
                      tctaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacattaacatatgagccccttcctttatggcaataggagaaaatgaagcagcttctctaataatgctcttccaattatgttgttgcagGAGCTATGTACTCTTTCCCCCAAATACGCTTACCACCAAAAGCTATAGATGCAGCCAAAAGGGCTGGCAAAGCGGCCGATGTTTTCTACTGCCTCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT