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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctcattcccattctttgttaacatatgatgagcagattttggaattgattttctgcagatgtagcaaataaaacaacaccttgattttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGACGACTTCACACG

Basic information

species Oryza sativa
transcript LOC_Os04g36050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 4
gttctcattcccattctttgttaacatatgatgagcagattt-tggaattgattttctgcagatgtagcaaataaaacaacaccttgattttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGACGACTTCACACG
||| |  ||  ||| ||||||              || |||| ||| |||    || |        ||| || ||||      |||||   |||||||||||||||||| ||||  || ||||||||||| ||   ||||||||| |||||||||||||||||||||||||||||||||||||| || ||||||||
gttattgttttcatcctttgtcgct----------caaatttatggtatt--ccttgtatcttccaagctaacaaaattcttacttga---tctgcagGAGAATAAAGAATCTGAGGATAAAGATGAGGGTCCGACTGAATATATATCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGAAGATTTCACACG

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G437119_T01 (Zea mays), 3'ss of exon 4
gttctcattcccattctttgtta----acatatga-tgagcagattttggaattgattttctgcagatgtagcaaataaaacaacaccttgattt--tctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGACGACTTCACACG
||| | |||  ||| |||||| |      || |||   | ||  || ||| |||   |||      || |  |||   || ||| | | | ||||  ||||||||||||||||||   ||  || ||||||||||| ||   ||||||| | |||||||||||||||||||||||| ||||||||||||| |||||||||||
gttgttattttcatcctttgtcactcagtatgtgaactaccaacttatggtatttgctttt-----atcttccaagctaa-caaaatcctaatttggtctgcagGAGAATAAAGAACTTGAGGATAAAGATGAGGGTCCGACTGAATATTTATCTTATTGGAAACCAAATGTAACAGTAAATCTTGTTGAAGACTTCACACG
















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|58607128|gb|CK035161.1|CK035161
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|33675031|gb|CF303270.1|CF303270
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|29683509|gb|CB679784.1|CB679784
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|58609841|gb|CK037874.1|CK037874
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|109974448|gb|DT806914.1|DT806914
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|84117031|gb|CD150798.1|CD150798
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
EST: gi|33677398|gb|CF305637.1|CF305637
EST:     AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAG                         GAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT
genomic: AGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCT

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: 67 (upstream exon), 62 (downstream exon)
Score: 28

CTGTTGTGGCTTACTTGCGAAAACCAAAAGATGGTAAAAAGAAGAGCTTGCTGGGAGATTCAAGTGAATCTAATGAACAACCACCACCTAAGgttctcattc ... ttttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGACGACTTCACACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaattgattttctgcagatgtagcaaataaaacaacaccttgattttctgcagGAGAATAAAGATTCTGTAGACAAAGATGAGGGCCCAGTTGAATATATTTCTTATTGGAAACCAAATGTAACAATAAATCTTGTTGACGACTTCACACG
                                             ttttctgc  CT-rich tract
                          aaataaaacaa  TA-rich tract