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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG

Basic information

species Oryza sativa
transcript LOC_Os03g62640.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069916_T01 (Zea mays), 3'ss of exon 9
gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
||||| | || |||||| || | ||| ||   | |    |    ||| ||| |||                 | | | ||  | |||  | |  | |  |||||||||||| ||||||||||||||||| || ||  ||||  | || |||||||||||||||||||||| ||||||||| |||
gtaatgc-ttctagctctttgttctctcatt-tatctcaagctgtcaaattgaat-----------------attttatcctaagcttaaatacaccaacagTGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G118014_T05 (Zea mays), 3'ss of exon 9
----gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgct-atattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
    ||   | |  |  |   |||||   || |   |   |   ||||| || |   ||  |   ||||| |  |   |   ||  | ||| | | | | ||  |||||||||||| |||||||||||||||||||| || || ||| | || ||||||||||||||||| |||| ||||||||| |||
acttgtgggttccatcgg--gcttttatccctagcctacccc--aacttgat-taggataaaaggctttgtt--gttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069916_T04 (Zea mays), 3'ss of exon 9
gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG------------------
||||| | || |||||| || | ||| ||   | |    |    ||| ||| |||                 | | | ||  | |||  | |  | |  |||||||||||| ||||||||||||||||| || ||  ||||  | || |||||||||||||||||||||| ||||||||| |||                  
gtaatgc-ttctagctctttgttctctcatt-tatctcaagctgtcaaattgaat-----------------attttatcctaagcttaaatacaccaacagTGATCGACGTCTTGCTGACCATTTTGGTGGGAAATTACACCTAGGCTACATGCTGATTCGTGAGAAACAGAAAGAACTTCAGGTAAATTCCTGCATGCTC

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G118014_T02 (Zea mays), 3'ss of exon 9
----gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgct-atattgtatc--cagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG------------------
    ||   | |  |  |   |||||   || |   |   |   ||||| || |   ||  |   ||||| |  |   |   ||  | ||| | | | | ||  |||||||||||| |||||||||||||||||||| || || ||| | || ||||||||||||||||| |||| ||||||||| |||                  
acttgtgggttccatcgg--gcttttatccctagcctacccc--aacttgat-taggataaaaggctttgtt--gttgttgatcctaagctgaaaatatctcaacagTGATCGACGTCTTGCTGACCATTTTGGAGGGAAACTGCATCTAGGCTACATGCTGATTCGTGACAAACAGAAAGAACTTCAGGTAAATTCCTGCATGCCT

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S402_41V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtat-------ccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
       ||| ||     ||  |        || || | | |      | ||||| |   |   |||| ||    |||  |  |||  |  ||  |        |||||| || ||| | || |||||||||||||| ||||| |||||||| || |||| |||||||||||| ||    ||  | | |
------tcttctaatgggttcagaaggacttatctttt-agatgctgcacttaatgctgccaagtggtgggtttcatgattagtgccttgctgcttaatactttcagTGACCGTCGCTTGGCGGACCATTTTGGAGGGAAGCTGCATTTGGGTTATATGCAGATTCGTGAGAAGCTCGTTGACTTGCGG

upper sequence: LOC_Os03g62640.2 (Oryza sativa), 3'ss of exon 9
lower sequence: PP1S88_36V6.1 (Physcomitrella patens), 3'ss of exon 9
-gtaattccttttagct--ccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
  |  |  |||| |     |  | |  ||    | ||  |  |    |       || |      |||  |    | | | | |  |||| || |   | |||||| || ||||| || |||||||||||||| |||||||||||||| ||||||| |||||| ||||| ||    ||  | |  
ttttctggctttcaaaagacgatattttcttttactgcccc-acgtgttgctgccaagtagtgggtttcatgatgagt-tcttttttgct-taatactttcagTGACCGTCGCCTGGCGGACCATTTTGGAGGGAAGCTACATTTGGGTTACATGCAGATTCGGGAGAAGCTTGTTGACTTGCGA

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|29665629|gb|CB661904.1|CB661904
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|86502553|gb|CI145186.1|CI145186
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|84117476|gb|CD151243.1|CD151243
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|454535|gb|D28304.1|D28304
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|86499113|gb|CI141746.1|CI141746
EST:     TTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: TTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|29664073|gb|CB660348.1|CB660348
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|29661288|gb|CB657563.1|CB657563
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACAT
EST: gi|29674744|gb|CB671019.1|CB671019
EST:     AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAA                         TGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTA
genomic: AAGTTGCGTCTCTGTGACATATGTGGAGCATTTCTAAGTGTCTACGACAAgtaattcctt ... ttgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG
   atttaat  putative branch site (score: 4)
                                         tatattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattccttttagctccttttgctcccaaaatgttctgaaacttcatatttaattcacacctttggtaggaaatatgtctcatgctatattgtatccagTGATCGACGCCTTGCTGACCATTTTGGAGGAAAGCTACATTTGGGATACATGCTGATTCGTGAGAAACTGAAAGAACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC