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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgctgattgcctgtgaaattatctcgagataattgcttattttctaccttcttgagctatgaagactaatatctgcggaatacatgaatttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAAAAAGAAGAGGGAAGAAGCGAAGGCTGCTGCAGCAGCTCGTGTCCAAGCC

Basic information

species Oryza sativa
transcript LOC_Os05g38370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 4
ttatgctgattgcctgtgaaattatctcgagataatt-gcttattttctaccttcttgagctatgaagactaatatctgcggaatacatgaatttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAAAAAGAAGAGGGAAGAAGCGAAGGCTGCTGCAGCAGCTCGTGTCCAAGCC
 |||||      ||| || ||  |  |  || |  || | ||  |      ||    |   |||   ||  |  |  |     || ||| ||| |    || ||||| |||||||| || |||||||||||||| ||||| || || ||||||||||||||||| ||||||||||| || |||||||| || || ||||| 
gtatgcaccgcacct-tgtaaccaaatatagtttgttcgtttgatcagagtctaagagttatatagtgatcataaagtaatagatgcataaatctgtgcagAGAACTTAAGAAGCAACGGGAGCTAGCTGCTGCTACCAAAGAAGAGGAGAAAAAGAAGAGGGAGGAAGCGAAGGCCGCGGCAGCAGCCCGGGTGCAAGCA
















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|88282653|gb|CI404049.1|CI404049
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88838265|gb|CI373625.1|CI373625
EST:     GGAAA-GTTCAAGCCTGGGCGGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTCCCACCAAGGAGGAAGAGAA
genomic: GGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88487060|gb|CI424331.1|CI424331
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|25044727|gb|AJ420710.1|AJ420710
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88204275|gb|CI204124.1|CI204124
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88209738|gb|CI209587.1|CI209587
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|14571477|gb|BI118845.1|BI118845
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCCACCAAGGAGGAAGAGA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCC-ACCAAGGAGGAAGAGA
EST: gi|88836064|gb|CI371169.1|CI371169
EST:     -GAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGGCCAGGCTATA                         GGAACTAAAGAAGCAGCGA-ATCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: GGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAA-GCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|38477260|gb|CF961393.1|CF961393
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCT
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCT
EST: gi|88267523|gb|CI379458.1|CI379458
EST:     A-GAAAGGTTCAAGCCTGGGCACTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|109711641|gb|CI013246.1|CI013246
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|86417638|gb|CI031847.1|CI031847
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88281942|gb|CI403338.1|CI403338
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88513582|gb|CI441088.1|CI441088
EST:     GTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
genomic: GTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAA
EST: gi|88980703|gb|CI022414.1|CI022414
EST:     AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA                         GGAAC-AAAGAAGCAGCGAGAGCTAG-T-CTGCCACCCAAGG
genomic: AGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAgtaagatgtt ... atttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACC-AAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaccttcttgagctatgaagactaatatctgcggaatacatgaatttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAAAAAGAAGAGGGAAGAAGCGAAGGCTGCTGCAGCAGCTCGTGTCCAAGCC
                     gactaat  putative branch site (score: 2)
                                              tttcctt  putative PPT
                      actaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgctgattgcctgtgaaattatctcgagataattgcttattttctaccttcttgagctatgaagactaatatctgcggaatacatgaatttccttagGGAACTAAAGAAGCAGCGAGAGCTAGCTGCTGCCACCAAGGAGGAAGAGAAAAAGAAGAGGGAAGAAGCGAAGGCTGCTGCAGCAGCTCGTGTCCAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC