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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccctgactaatctcttcagtcattacgagtaaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacattttttccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC

Basic information

species Oryza sativa
transcript LOC_Os03g46740.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g46740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 8
gtataccctgactaatctcttcagtcattacgagtaaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttg-atattatacattttttccatta-cagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC
          | | ||    | ||  |  |   |    || || |  |  || |  ||| |   |     ||| |   |   |  |  || |  |   |          ||||||| ||||  |   ||||  |||| || ||||| ||||| ||||| || ||||| |||||||| || || || ||||||||||||||||| || ||| | || ||    ||||| |
--------gtattgatg--atgagctaaga-aggcgttttcctctttttatt-atcggatatatactctgaactggaaaggctgtttctgtccataagcagacgctccttacatttcttcctctggtagGTCCTTTTATATGATGAACCTACAGCTGGGCTCGACCCGATTGCATCAACTGTCGTGGAAGACCTTATACGTTCTGTGCATATGACTGGACGGGATGCCC

upper sequence: LOC_Os03g46740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 7
gtataccctgactaatctcttcagtcattacgagtaaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacattttttccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC
                 | || |    | | ||   || |  |    |  ||||    |||       |   |  |||| ||   |  ||  | |    |  | ||| |  | || |     || ||||  | ||||| || || || |||||||||||||| || |||||||| || ||||||||||| || || || || || ||  ||| |||  |||||||  
---------------ctttttgaaatctcatgatataacttttactgttattcaatcaaaa-------ccctccccttatctcttttctgtttataaaataaacattttgtacttctg----tataGGTGCTCTTGTATGACGAACCAACTGCTGGACTTGATCCCATTGCATCTACTGTTGTTGAAGATCTGATTCGCTCTGTGCACATAAAAGGACAAGATGCA-

upper sequence: LOC_Os03g46740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 7
gtataccctgactaatctcttcagtcattacgagtaaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacatttt---ttccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC
                             |    | |  || | ||| | ||      |   |   | ||   | |      | || |    | | ||  | | |  |  ||||||    | |  |||||||  | ||||| || || || |||||||||||||| || |||||||| || ||||||||||| || || || || || ||  ||| |||   |||||| |
-----------------------------aaatctcatatgatataacatttacttttattcgatcaacatgtacccacctcttctgtcttttctgtttataaaac-aagcattttgcacttctgtacagGTGCTCTTGTATGACGAACCAACTGCTGGACTTGATCCCATTGCATCTACTGTTGTTGAAGATCTGATTCGCTCTGTGCACATAAAAGGACGAGATGCAC

upper sequence: LOC_Os03g46740.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------gtataccctgactaatctcttcagtcattacgag-taaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacattttttccattac--agGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC
                  ||   | |  ||| | ||   || |||   | |  | | ||| |   ||  |       | || |   ||   | | |  |   |   | |      |   |  |     |   | || || |  ||||  |||||||||||||||| |||||||||||||| || |||||||| || || |||||||| |||||||| || || ||  | ||||   |||||||  
gtaatcttaatatctacttaagttcatgaatgtgtttcttctttagaggcttgactcctgcatctgtatagttattgatgaaacttaaagtcatcatgtggcaaaaattaggaattcatttatgggtttcactgccttttcttagGTGCTTTTGTACGATGAGCCAACTGCTGGACTTGATCCAATTGCATCAACTGTAGTTGAAGATCTTATACGGTCTGTTCACATGACAGACGAAGATGCAG

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|27921057|gb|CB096865.1|CB096865
EST:     TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAG                         GTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
genomic: TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAGgtataccctg ... tccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
EST: gi|58691671|gb|CK080358.1|CK080358
EST:     TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAG                         GTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
genomic: TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAGgtataccctg ... tccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
EST: gi|226698432|gb|GO497010.1|GO497010
EST:     TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAG                         GTTATTTTGTAC
genomic: TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAGgtataccctg ... tccattacagGTTATTTTGTAC
EST: gi|58593744|gb|CF992052.1|CF992052
EST:     TAGCTCGTTCAATAATGTGCGATGATACAAAGGAAACAATAGAGCCAGAG                         GTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
genomic: TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAGgtataccctg ... tccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
EST: gi|27547660|gb|CA767399.2|CA767399
EST:     TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAG                         GTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC
genomic: TAGCTCGTTCAATAATATACGATGATACAAAGGAAACAATAGAGCCAGAGgtataccctg ... tccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcttaacttactattgactgtcttcttgatattatacattttttccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC
                                        ttttttccatt  CT-rich tract
                        ttcttgatattataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataccctgactaatctcttcagtcattacgagtaaattgctgtaatagttcacaggaaaaggagatcaaacagcttaacttactattgactgtcttcttgatattatacattttttccattacagGTTATTTTGTACGATGAGCCTACTGCTGGACTTGACCCTATTGCATCCACCGTTGTTGAAGACCTTATACGTTCCGTACATGTAACAGGGAAAGATGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG