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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA

Basic information

species Oryza sativa
transcript LOC_Os02g47440.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G108087_T01 (Zea mays), 3'ss of exon 4
cttattt-tgattgata-ttcatggtgataaaatacgacatgcaagatt-tggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
   || | ||||  | | ||     | |  |   |  |  || |  ||  || |   |    |||| | ||  | |||| | | ||  ||||||  |||  || |||||||||||||||||||| ||||||||||||| |||||||||||| |||||||||||||||||||| ||||||||||| ||||| ||||||||||||
---atgtgtgataaaaactttgacatcactagcaagaatttgtagaatcctgtttccaaatttttttcctagttttctgatgaatttccatgttactctgaagACAAGAGGTGCTGCAATTGGACAATGAAATTGTTTACAATGAAGCTATAATTGAGGAAAGGGAGCAAGCCATTCAAGATATCCAACAGCAGATTGGTGAA

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G13410.1 (Glycine max), 3'ss of exon 4
-cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
   ||  |  |    |        | ||   ||   |  |   | |||    | | |   || |     || ||  ||||    || || |  | || |||||| |||||  |    || |||||||| ||||  |||||||| |||||||||||||||||||||||||  |||||||| || || || || |||||||||
aagtagatgaacaactgaattcatttatgttattaaaattttcaaattctccacattgcattatttcagcaccttagctattgcattat-tcatgctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAGCAGCAAATTGGTGAA

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G33950.1 (Glycine max), 3'ss of exon 4
-cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgttttt-cttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
   ||  |  |||  || |    |  ||| || || || |   | |||||    | |  | ||   |||  |  ||  |   ||    | ||  | |  ||| || || ||  |    || |||||||| ||||  |||||||| ||||||||||| ||||| || |||| ||||||||| |||||    || |||||||||
ctgtacatgcatttgtaataccagatatagaagactacttatcaaatttgacc-atttgcattattttat-ttcctaatctcttgcattattgatgccacagACAGGAAGTATTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATCATTGACGAAAGAGATCAAGGTATTCAAGAAATTCAGTCGCAAATTGGTGAA

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G08200.1 (Glycine max), 3'ss of exon 4
-cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
   ||  |  |    |        | ||   ||   |  |   | |||    | | |   || |  |   | ||  ||||    || || |  | || |||||| |||||  |    || |||||||| ||||  |||||||| ||||| |||||||||||||||||||  |||||||| || ||||| || |||||||||
aagtagatgaacaactgaattcatttatgttatcaaaattttcaaattctccacattgcattattttagtaccttagctattgcattat-tcatgctgcagGCAGGAGGTTTTATTCTTAGATAATGAGATTGCCTTCAATGAGGCTATTATTGAGGAAAGGGAGCAAGGCATTCAAGAAATACAACAGCAAATTGGTGAA

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G01960.1 (Glycine max), 3'ss of exon 4
cttattttg-attgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgttttt-cttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
|| |   || |||  || |    |  ||| || || || |   | ||| |    | |  | ||   |||  |  ||  |   ||    | ||  | |  ||| || |||||  |    || |||||||| |||   |||||||| ||||||||||||||||| |||||||  |||||||| || ||    ||||||||||||
ctgaacatgcatttgtaataccagatatagaagactacttatcaaattcgacc-atttgcattatgttat-ttcctaatctcttgcattattgatgccacagACAGGAGGTATTATTCTTAGATAATGAGATTTCCTTCAATGAGGCTATCATTGAGGAAAGAGAGCAAGGCATTCAAGAAATCCAGTCGCAGATTGGTGAA

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0039g01850.t01 (Vitis vinifera), 3'ss of exon 4
-----cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
     || || ||  |   | |  || | | |  || ||   ||  |  || |  || |||   ||| |  |  | |  |  |   | ||  || |||  | ||| || || ||  ||  |||||| ||||| ||    ||||||||||| || ||||| ||||| |||||||  || ||||| ||||| |||||||||||||| 
gggaactcatctttctaagtctagatcgagtttgaacacattat-taccatat--tataatgcttttactatgaaaccgtagtttctaat--tgatttagtgcagACAGGAAGTTGTGTTATTGGACAATGAGATCACCTTCAATGAAGCCATAATTGAAGAAAGAGAGCAAGGAATCCAAGAAATTCAGCAACAGATTGGTGAG

upper sequence: LOC_Os02g47440.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0012g01850.t01 (Vitis vinifera), 3'ss of exon 4
cttattttgattgatattcatggtg-ataaaatacgacatgcaagatttggtagaatcacttttccttacat-----ctctgctaagttatcatgttttt----cttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
         | ||     ||||    | |  |||  |  |  | |  ||   |||||   || | || | ||     |||  ||||  ||| |  |  ||    || ||| || |||||  ||   ||||| ||||| ||||| |||||||| ||||||||||| ||||||||||| |  || ||||| || || || || ||||| || 
-------aaactgg-gcacatgccctacattatatcatttctaggcatta--agaataggttcttctaatatgctctctcccctaaactattagatgatttgtgctgcagACAGGAGGTCTTGTTGTTGGACAATGAGATTGTCTTCAATGAGGCTATCATTGAAGAAAGGGAGCAGGGAATACAAGAAATCCAGCACCAAATTGGCGAG

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|313084008|gb|HO213791.1|HO213791
EST:     GATTCTGGTAAAATTCCTGAACAGCATGCGCTACTCGCAGAATCAAAGAG                         GCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCAT
genomic: GATTCTGGTAAAATTCCTGAACAGCATGCGCTACTCGCAGAATCAAAGAGgtcagtgttc ... ttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCAT
EST: gi|58606351|gb|CK034384.1|CK034384
EST:     GCTACTCGCAGAATCAAAGAG                         GCAAGAGGTGCTGCAATTGGAT-ATGAAATTGTTTTGAAGTGAAGCTATCA
genomic: GCTACTCGCAGAATCAAAGAGgtcagtgttc ... ttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAA-TGAAGCTATCA
EST: gi|29646264|gb|CB651271.1|CB651271
EST:     GATTCTGGTAAAATTCCTGAACAGCATGCGCTACTCGCAGAATCAAAGAG                         GCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCAT
genomic: GATTCTGGTAAAATTCCTGAACAGCATGCGCTACTCGCAGAATCAAAGAGgtcagtgttc ... ttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA
                 tccttac  putative branch site (score: 2)
                                       tcatgtttttcttc  putative PPT
                                taagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttattttgattgatattcatggtgataaaatacgacatgcaagatttggtagaatcacttttccttacatctctgctaagttatcatgtttttcttcagGCAAGAGGTGCTGCAATTGGATAATGAAATTGTTTTCAATGAAGCTATCATTGAGGAAAGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT