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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT

Basic information

species Oryza sativa
transcript LOC_Os01g10050.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacattt----ttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
||| ||| |  |        | |||  ||    ||||     |  || |||    ||   |    ||  |   |||| ||    ||  || |||| || |||| ||||||||||||||||||||  |||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| ||
gtgagaacttgtttccccaatgcttttcc----ttctcaaccatcttttgggaa-ctccagctaaaaattctgaacacttacaattttgt-tgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 3
gtgcgaaatgttgcttatgtttcttaaccgatt---ttcttggatacat-tctggacttcttttgtggtaat-ctactaacatttt----tccgtgtgttattaa-------agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
  | ||     |    |     || |   ||||   ||      | ||| |  ||    ||||| ||   || ||||     ||||    ||| |  ||| | ||       ||  ||||| ||||| |||||||| || || || || || || |||||||||||||| || ||||| |||||| | ||||| |||||||| ||||| |  ||
--gtgagtatataaggaaacaactgagatgattagatttcacattgcatgtaagggtgccttttctgactatgctacctttgttttgccgtccattcgttttcaatattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 3
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaa-agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
                                      || | | || |     | | ||    |  |||         ||    |  | ||||   ||  ||||| ||||| ||||||||  | || || || || || ||||||||||| || || ||||| |||||||| ||||| |||||||| ||||| |  ||
----------------------------------gtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
-------------gtgcgaaatgttgc--ttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaa-agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
             |    || ||   |  |||  |||| ||   ||| |    || | | || |     | | ||    |  |||         ||    |  | ||||   ||  ||||| ||||| ||||||||  | || || || || || |||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| |  ||
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaa--gggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaaa-------gCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
  |  |    |   || || | ||  |    |||| ||       ||  |  ||| |||  ||| | |     ||   | | | |  ||  || |||       || | ||| || || ||||| ||  ||||  | || || || |||||||| |||||||||||||||||||||||| |||| |||||| | || ||||||||
--gtaatgcttgatttctgctcctggagttctttttttt------tttcgttcttgtttgatggaagttgtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtgcgaaatgttg-cttatgtttcttaaccgattttcttggatacat-----tctggac-----ttcttttgtggtaatctactaacatttttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
                              || || |  ||  || | | | |  | | || |   |  ||| ||     | || ||     || |||| | || |     |    | ||||  ||| || |   ||| || || ||||| ||||||||  | || ||||| || || |||||||||||||| |||||||| ||||| ||| |||| |||||||| ||||| |  ||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatctatctatatatatatatatatgcacacacatttttttctagttacaagttttggtctttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGAT

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|218490551|gb|FG953048.1|FG953048
EST:     CTTTTACCTGCCATTGTTCATGTTAATGCTCAGCCGATTCTAG                         CACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTG
genomic: CTTTTACCTGCCATTGTTCATGTTAATGCTCAGCCGATTCTAGgtgcgaaatg ... gttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
                          tactaac  putative branch site (score: 0)
                             taacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaaagCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG