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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaccaaaaataggaacatttgatgggcataaatgtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g07150.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112793_T01 (Zea mays), 3'ss of exon 1
-----------------tgaccaaaaataggaacatttgatgggcataaatgtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctca-attgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG
                 || ||||||  ||| | | ||| |  ||||| ||||   ||  |||         | |||  |||||||  | |     ||      ||| || ||| |||||||| || ||||||||||||||||||||||||||||||||||||||||| ||||||
cgtgctatgtttccgcttggccaaaagaagggatacttggt--gcatagatgt--gcaggacta--------acattattggaatcggcataatgact------cccacatatttcagGTTAAGGCCCTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG

upper sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G420926_T01 (Zea mays), 3'ss of exon 1
--tgaccaaaaataggaacatttgatgggcataaat----gtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctca-attgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG
  ||| |||||  ||||| | ||| |    | |       | || ||    || |||||| | |||| |||||||  | |       |  || ||| || ||| |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||
cttgagcaaaagcaggaatacttggtccatacatgctcaggactgca-ggttgatgttctaacattcttggaatcggcata------atgggtcccacatatttcagGTTAAGGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAACGTTCAG

upper sequence: LOC_Os03g07150.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S88_179V6.1 (Physcomitrella patens), 3'ss of exon 1
----tgaccaaaaataggaacatttgatgggcataaatgtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG
    |   |    |  ||  | ||  ||  || |  | |  | ||  |         | ||     ||| || |  |  ||   |  | ||     |||  ||||||| |||| ||||||||||||| |||||||| |||||||| || | ||||||||||
tagctcttccctcactggtgctttgcat--gcttggaagattgcaggaacataaaaatcattcagttgggatatctg-atgggttgttagagttgtaatc-cagGTTAGAGCATTGTGCGAGAAGGCGAAGGAGATCTTGATGGAAGAGAACAATGTTCAG

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|88300769|gb|CI589761.1|CI589761
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|29638619|gb|CB643628.1|CB643628
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|218480610|gb|FG959508.1|FG959508
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         G-TAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|218485818|gb|FG963200.1|FG963200
EST:     GCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAA-GAGATATTGATGGAGGAAAGCAAT
genomic: GCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|29617800|gb|CB622812.1|CB622812
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|29682371|gb|CB678646.1|CB678646
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|88402803|gb|CI613251.1|CI613251
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|29615298|gb|CB620310.1|CB620310
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|58680593|gb|CK069280.1|CK069280
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
EST: gi|58665829|gb|CK054515.1|CK054515
EST:     ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAG                         GTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT
genomic: ACACGCAGATCGAGCAGCTGATGCAGTGTCGCCCGCTCGCCGAGCAGGAGgtgagagcga ... tcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgttcttatattcctggaatctacgtgtgttctaatggaccctcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG
                                ttctaat  putative branch site (score: 2)
                                          ccctc  putative PPT
     ttcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaccaaaaataggaacatttgatgggcataaatgtctacacaactggtgttcttatattcctggaatctacgtgtgttctaatggaccctcaattgcagGTTAAAGCACTGTGCGAGAAGGCCAAGGAGATATTGATGGAGGAAAGCAATGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
-gaccaaa
- - - - aataggaa
- - - - - - - - - -ttgatgg
- - - - - - - - - - - - - - - - - - ctacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaccc