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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttcttgcatcatgtatcttaagcacagttttaatttccataattgatgattctactggtgggcaatatgacattcacttgtctttgttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGCAGTGATGCACCGCCGACGCCAGAGGCAGCAAATACCACCGCAGCATCTA

Basic information

species Oryza sativa
transcript LOC_Os03g58480.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G163912_T02 (Zea mays), 3'ss of exon 5
--ttatttcttgcatcat-gtatcttaagcacagttttaatttccataattgatgattctactggtgggcaatatgacattcacttgtctt-tgttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAG------GAGGAGGAGCTGCAGTGATGCACCGCCGACGCCAGAGGCAGCAAATACCACCGCAGCATCTA
   ||    | |||| || ||  |||  |    |  |  ||  | ||| ||   |||  | ||| |||  ||  |   |||   ||| ||| |||||  | ||||| ||||| |||||||| ||||||||||||||||||||      ||| | |||||||| |||  |||| | ||| || |||| |  ||| |||| ||||       
aagtagaaat-gcatgattgttgcttgtggcatgaatacatcgcgatacttttcgatggttctgatggtgaaatt---atttttttgccttctgttccgtcaagGTGCCTCCTACTCGTGCCAAATCACCAAAGTTTACAAGCTCAAGGAGAAAGAGCTGCAATGACACACCACAGACACCCGAGGGAAAAAACACCAACGCAA------
















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|58669319|gb|CK058005.1|CK058005
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|58684814|gb|CK073501.1|CK073501
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|86412782|gb|CI067187.1|CI067187
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|88245064|gb|CI244913.1|CI244913
EST:     AAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: AAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|88840896|gb|CI080350.1|CI080350
EST:     ACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: ACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|16754058|gb|BM038437.1|BM038437
EST:     TCCTCC-AAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCGAAGTTTACAAGGAGGAGGAGCTGC
genomic: TCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|89183694|gb|CI046259.1|CI046259
EST:     TGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|86412638|gb|CI067043.1|CI067043
EST:     AGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: AGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|58686125|gb|CK074812.1|CK074812
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAGAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|8335160|gb|BE040144.1|BE040144
EST:     CTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: CTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|58597056|gb|CK007584.1|CK007584
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTCAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|29687299|gb|CB683574.1|CB683574
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|218500899|gb|FG952816.1|FG952816
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|29628405|gb|CB633416.1|CB633416
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|27554048|gb|CA997948.1|CA997948
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|29659604|gb|CB655879.1|CB655879
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|58677015|gb|CK065702.1|CK065702
EST:     GCTTCTA-CAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: GCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|29643448|gb|CB648455.1|CB648455
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|38481034|gb|CF965123.1|CF965123
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|88990034|gb|CI107501.1|CI107501
EST:     GCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: GCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|2310662|gb|C26817.1|C26817
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|88832373|gb|CI019314.1|CI019314
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
EST: gi|88223481|gb|CI223330.1|CI223330
EST:     TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAG                         GTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC
genomic: TGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGC

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: 75 (upstream exon), 75 (downstream exon)
Score: 82

AACAGCCTTAAAACAACTAAGAAAGTCCTTAGTCATCAGGGCAAAGCCCATGCCAAGCTTCTACCAAGAAGGACCTCCTCCAAAGGCTGAACTTAAGAAGgtagttctga ... ttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGCAGTGATGCACCGCCGACGCCAGAGGCAGCAAATACCACCGCAGCATCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgattctactggtgggcaatatgacattcacttgtctttgttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGCAGTGATGCACCGCCGACGCCAGAGGCAGCAAATACCACCGCAGCATCTA
 aattgat  putative branch site (score: 82)
                                   cttgtctttgttcttt  putative PPT
                      aatatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttcttgcatcatgtatcttaagcacagttttaatttccataattgatgattctactggtgggcaatatgacattcacttgtctttgttctttgaagGTCCCTCCAACTCGTGCTAAATCACCAAAGTTTACAAGGAGGAGGAGCTGCAGTGATGCACCGCCGACGCCAGAGGCAGCAAATACCACCGCAGCATCTA

- - -tcttgca
- - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - - - - - ttgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acattca