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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G165418_T04 (Zea mays), 3'ss of exon 6
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcattt---aattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
   |    | |  | |    || | |||||| |||||| |||||||||   |||||||  ||||||  ||||     |   | | | ||||   ||| | ||||||||| ||||||| |||||||||||||||||| || |||||| ||||||| ||||| ||||| | ||||||||| || |||||||| ||||||||| ||
---ttaatattcctgcagggtgcagattccaaatacttcttcaatgataacatttgtgggcattgtattgatacatattcttgtattatttgttaatcgacagTGATGGTGAGACATTCATATCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaat----ttgtgaacattgtgctgatttgctt----ctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
       |  | | ||||| || || ||    | | |||||   | || | ||    || |  | | ||  |  |||||  |     | | || |   ||  |  ||| |||||||| || | ||||||||| ||||||||||| |||||||| |||||  |||| || |  || || || || ||||||||||| || |||||| ||
-------ctttatgtctacatg-attttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
---------ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcatttaattgt--cagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
         || ||   | | ||  |     || ||| || | |||| |  | ||   |  |||||   | ||||| | ||         |  |||  ||||||||  |||||| || || || |  || || || |||||||||||  ||||||| ||||||||||| || |  |||||||| |||||||||||||| || |||||  ||
ttattctctttgtcgaaaatcttgttgatcctaaatttcaca-acttgt--attgcattgttttgt--tccttgtggtaatgaa------tcgttcccttaattgttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 6
ttatctgcagtttttctacctgta-tattccatatactttttcaatgatc--taatttgtgaacattgtgctgatttgcttctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
  |  || ||   |  || |   | ||||| | ||||| | |  |   |   | | |||| |  | | |  |    | ||  | || | | || | |    |||||||| ||||||| ||||||||| |||||||| || ||||| || |||||  |||| || |  || || || |||||||||||||| ||||||||| | 
--acatggagccatattatccacactattctacatactgtctgcacttttagtcacttgtaagaaat-taatagactactaattttatcctttcattctcaagTGATGGAGAGACATTCATATCAGCTGATGATCTACGCATAAACCTTTGGAACCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTGAAGCCTACT

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttct--ctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
  |    |  || |   | |  |        || |||| || | |  ||| ||||| | ||  | |  |||  |  | ||   | ||||  |   |   ||||||||| || ||||  |||||||| ||||||||||| ||||| || ||||| ||||| || |  ||||| ||||||||||||||||| ||||||||| ||
-gaaagactattatggaaacaatgctaatggta-acttgtttatttctcttatttgggtacgatttagtgaaattttgctgattgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

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|2310581|gb|C26736.1|C26736
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     ATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: ATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|58588909|gb|CF987217.1|CF987217
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAT
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
EST: gi|33796287|gb|CF324010.1|CF324010
EST:     GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAG                         TGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA
genomic: GTATATGCACATGCTCATGATTACCATATTAACTCTATATCAACCAATAGgtaagtatga ... taattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctaatttgtgaacattgtgctgatttgcttctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA
                          tttgcttctctttttc  CT-rich tract
                                  tctttttcatttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctgcagtttttctacctgtatattccatatactttttcaatgatctaatttgtgaacattgtgctgatttgcttctctttttcatttaattgtcagTGATGGCGAGACATACATATCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC