Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgctaacactgtttgatgtccttccatgctgaaagattaagatattgatttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT

Basic information

species Oryza sativa
transcript LOC_Os06g22650.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------------------gtctgctaacactgtttgatgtccttccatgctgaaagattaagatattg----atttattgttttgttt----tctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                                                                                          |  |||     |  |   |      || |  | |   || || ||| ||    || || | ||| ||||    | |||||||| ||||| || |||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||| || ||||| | |||||
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT

upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 3
------------------gtctgctaaca-ctgtttgatgtccttccatgctgaaagattaagatattgattta--ttgttttgtt--ttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                   | |  |  || || | ||||||   |   | ||  | |   || || ||||| |   ||||  ||    || |||||||||| |||||| ||||| ||||||||  ||||  |||| |||||||||||||||||||| ||  |  | ||||||||||| ||||||||||  ||||
gtatacataatttcttgaatatttttgcagctttctgatgtttctgttttcttcatgtaaaatatgttgatgtgatttgtcatgccaattgtagCCTGATTTTCATGTCAAAGAAAAGATACTGGTTCTTGTAGATACTTGGCAAGAAGCTTTTGGAGGCCCAAGGGCAAGATATCCACAATATTATGCTGCAT

upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
----------gtctgctaacactgtttgatgtcc--ttccatgctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
             ||  |   || ||| ||  |   || |||  |||||  |     |||   ||||||        ||  ||||||||||| ||||| | |||||||||| | ||||| ||||| |||||||||||||||||||| ||  |  | ||||||||||| || ||||||| |||||
gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattg-tagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
-------------------gtctgc-taaca---ctgtttgatgtcc--ttccatgctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                   || | | || |    || ||| ||  |   || |||  ||||| ||     |||   ||||||        ||  ||||||||||||||||| | |||||||||| | ||||| ||||| |||||||||||||||||||| || ||  | ||||||||||| || ||||||| |||||
gtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattg-tagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 3
------------------gtctgctaacactgtt-tgatgtccttccatgctgaaagattaagatattgattta--ttgttttgtt--ttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                   | |  |  || | || | |||||  |   | ||  |  ||  | || ||||| |   ||||  |     || |||||||||| |||||| |||||||||||||| ||||| ||||| |||||||||||||||||||| ||  |  | ||||||||||| ||||||||||  || |
gtatacatagtttcttgaatattttttcagttttctaatgtctctgttttcttcat-atatatatgttgatgtcatttgtcataccaattgtagCCTGATTTTCATGTCAAAGAGAAGATACTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGCCCGAGGGCAAGATATCCACAATATTATGCTGCTT

upper sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtctgctaacactgtttgatgtccttccatg-ctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                          | |  |  |   |||| || |  || | |  | || | |       || | ||||||| |      ||  |||||||||  ||||| | |||||||||| | ||||||||||| |||||||||||||||||||| ||  |  | ||||||||||| ||||| ||||  ||||
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattctgcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|29622891|gb|CB627902.1|CB627902
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88449216|gb|CI565862.1|CI565862
EST:     TTGCTGAGAGGGATATAGTCGATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGAT-CTAATTCTGATAGACACTTGGGAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|300215825|gb|HO088451.1|HO088451
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88395584|gb|CI613106.1|CI613106
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGAT
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGAT
EST: gi|88743810|gb|CI765396.1|CI765396
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATG
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATG
EST: gi|58682180|gb|CK070867.1|CK070867
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88372781|gb|CI612709.1|CI612709
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATG
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATG
EST: gi|58668792|gb|CK057478.1|CK057478
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|58670501|gb|CK059187.1|CK059187
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88362739|gb|CI608888.1|CI608888
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCA
EST: gi|88363491|gb|CI618052.1|CI618052
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAAT
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAAT
EST: gi|58668384|gb|CK057070.1|CK057070
EST:     GGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: GGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|87017040|gb|CI286176.1|CI286176
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88417416|gb|CI579077.1|CI579077
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAA
EST: gi|29630559|gb|CB635568.1|CB635568
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG                         CCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAA
EST: gi|88406396|gb|CI596523.1|CI596523
EST:     TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTACGAAAAAG                         CCTGATTATCATGTAAAAGA
genomic: TTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 57 (upstream exon), 71 (downstream exon)
Score: 18

TTGCTGGAGACACTGATTAAAAATTGTGGAGACTTTGTTCATATGCACGTTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAGgtctgctaac ... tgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtccttccatgctgaaagattaagatattgatttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
                             tattgat  putative branch site (score: 18)
                                       ttgttttgttttct  putative PPT
                      attaagatattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgctaacactgtttgatgtccttccatgctgaaagattaagatattgatttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA