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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacctcaataattttccctcatagtcatgtgtcatcggattcttaaaatgctatacattctgtttcttgattgttttttctggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG

Basic information

species Oryza sativa
transcript LOC_Os07g43390.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G013811_T01 (Zea mays), 3'ss of exon 7
gtacacctcaataattttccctca-tagtcatgtgtca-----tcggattcttaaaatgctatacattctgtttcttgattgttttttctggt-gtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
|||  ||||||| |||||| |  |  | || |   |       | ||   |||  |||  | |   || || ||||| | |||  | |||||| ||||||||||| || ||||| || ||||| |||||||| |||||||||||||||||||||||||| ||||| || ||||||||
gtatgcctcaattattttctcaaagcaatcttacttttattgtttgggaacttgtaataat-tgtgttatggttctttactgtgctctctggttgtaaagGACAAAAACGGTTTCCCCACTTTCGTTAGTGGCGTTCCACCTGATGCATTTAGTGAAACGGGTCAACTATGGAACAG

upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100730_T01 (Zea mays), 3'ss of exon 1
gtacacctcaataattttccctca-tagtcatgtgtcatcggattcttaaaatgctata----cattctgtttcttgattgttttttctggt-gtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
||| |||||||| |||||| |  |  | || ||  |     | ||   || |||  |||      || || || || | | |  | |||||| | |||| ||||||||||||| |  | |||||||||||||||||||||| |||||||||||||||  ||||| || ||||||| 
gtatacctcaattattttctcaaagcaatcttgcttttattgtttgggaacatgtaatagttgttttatggttttttactatgctctctggttgcaaagAACAAGAATGGTTTCCTCAATTTTGTTAGTGGTGTTCCACCTTATGCATTTAGTGAAATGGGTCAACTATGGAACAA

upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G39730.1 (Glycine max), 3'ss of exon 6
----gtacacctcaataattttccctcata-gtcatgtgtcatcggattctt-----aaaatgctatacattctgtttcttgattgtttttt-ctggtgtaa-agGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
    |||   |  ||  | | || || |   || || || | |    || ||     |  ||  | ||| || || |  |  | |  | | |  |  | |   || ||| ||| || |||||   ||| |||||||||||||| ||||| ||||| |||||||||||||||||||||  |||
gttagtagttcctaaagaatgtctctgaagtgtgatctgacttttctttttttttggagcatattgtaccttttgatcataaaataatatctatttatctggcagAACAGGAAGGGCTTTCCTCTTTTAGTTAGTGGTGTTCCTCCTGACGCATTCAGTGAAACTGGTCAGCTTTGGGGCAG

upper sequence: LOC_Os07g43390.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0031g01540.t01 (Vitis vinifera), 3'ss of exon 7
-------gtacacctcaataattttccctcatagtcatg-tgtcatcggattcttaaaatgctatacattctgtttcttgattgttttttctggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
       || | | ||| ||| |||     ||  | ||  | |  ||     |||       | |   ||||  |     ||| |   ||   ||    || ||||||  ||||||||   | | |||||||||||||| || ||||| |||||||||||||| ||||| |||  |||
gttagtagttctcttcattaactttaagaaatcttaataatctagtcatgaccttc---cattctgagttctactgacaaattatcccttt--gttggcagAACAAGAGCGGTTTTCCTCTTCTAGTTAGTGGTGTTCCTCCCGATGCCTTTAGTGAAACTGGCCAGCTGTGGGGCAG

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|218503567|gb|FG951513.1|FG951513
EST:     TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTG                         GACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
genomic: TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTGgtacacctca ... tggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
EST: gi|218485155|gb|FG948396.1|FG948396
EST:     TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTG                         GACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
genomic: TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTGgtacacctca ... tggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
EST: gi|218501179|gb|FG958401.1|FG958401
EST:     GGAAATCGTTTTTGCTG                         GACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
genomic: GGAAATCGTTTTTGCTGgtacacctca ... tggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
EST: gi|27577080|gb|CA999774.1|CA999774
EST:     TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTG                         GACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT
genomic: TTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTGgtacacctca ... tggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTT

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: 70 (upstream exon), 75 (downstream exon)
Score: 28

ATATGCAAAGAAGTTGGGTATCAGCATAATGGGTGACATGCCCATATATGTTGGCTACCATAGTGCAGATGTTTGGGCAAACAGGAAATCGTTTTTGCTGgtacacctca ... tggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggattcttaaaatgctatacattctgtttcttgattgttttttctggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG
                             tcttgat  putative branch site (score: 28)
                                   ttgttttttct  CT-rich tract
                                  attgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacctcaataattttccctcatagtcatgtgtcatcggattcttaaaatgctatacattctgtttcttgattgttttttctggtgtaaagGACAAGAATGGTTTTCCGACTTTTGTTAGTGGTGTTCCACCTGATGCATTTAGTGAAACTGGTCAGCTTTGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT