Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC

Basic information

species Oryza sativa
transcript LOC_Os02g21970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 1
--ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
  |||   |  | || |     ||   | |   |   || | |  |   || |  |       | |     |||  |||| || | || | |   | | ||||||||||||||||||||||||||||| |||||||| |||||||| |||||||||||  |||| ||||||||| |||||||||||||||||||||||||||
ttctctagtggcttgtatggatttggctctaatttcatgaagtgcacctatgcctttagtt--tcagtgcattacaatttattggttttttatggtgtgcagGATATTGGAGGATGTGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAATTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G038126_T01 (Zea mays), 3'ss of exon 1
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatt-taacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
 ||  ||    || |    |||   | |   |   |  | |  |   || || |    |   |    |||  ||  ||  || | |||| |   | | ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||  |||| ||||||||| |||||||||||||||||||||||||||
ttctaatggtttgtaaggaattggctctaatttctttaagtacacctatgcatttagtat-cagtgcattacaattttcattggtttcttatggtgtgcagGATATTGGAGGATGCGACATCCAAAAGCAAGAAATACGGGAGGCGGTTGAGTTACCCTTGACTCATCATGAGTTGTACAAGCAGATTGGTATTGATCCTC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 1
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
  |  || |   | |  || |  |  ||       ||     | |   |    |  |           | |  | ||||  ||  | |||   |||| |||| |||||||||||||| ||||| ||||| ||||| || ||||| || ||  |||| || || |||||||| || ||||| || ||||||||||||||||
ggcctatgtttagtatattgtcaaacatgttgtcttgagggttttgttttttattaatggcatgttcttatccccttttcatgtatttgatattttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGCGAGGCCGTGGAGCTACCCCTTACGCATCATGAACTATACAAACAAATTGGTATTGATCCTC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 1
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatat--ttaacatttttt--tgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
     ||  |  | |  |||||   || |      | |   || ||| |  |||  |    |   || |  ||| |    |||  ||  | |||   |||| |||| |||||||||||||| ||||| ||||| ||||| || |||||||| ||  |||| || ||||||||||| || ||||| || ||||||||||||||||
----aattactggcatgttattatgtagtataatttatccccttttctttgagtttaattgttgcatgtccttatccccctttgatgtatttgatcttttttagGACATTGGAGGATGTGATATCCAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCTC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 1
--ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
  |  |  | |  |  |   |    | | |||      |   | | ||  |  | |      ||    | | |  | ||||  ||  | |||   |||| |||| |||||||||||||| || || ||||| ||||| || |||||||| ||  |||| || ||||||||||| || ||||| || ||||||||||||||| 
ggcctatgtttagtatattgtcaaaaatgttgtcttgagggttttgtttttttatttatggcatgttct-tatccccttttcatgtatttgatattttttaGGACATTGGAGGATGTGATATACAGAAACAGGAAATCCGTGAGGCTGTGGAGCTACCCCTTACACATCATGAACTATACAAACAAATTGGTATTGATCCT-

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 1
ctcacatatcctggagcttatttattattgct-cactgtaatctattcatacagtcgacaaataaaatatttaacatttttt-tgcttctgactattttc----agGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
 | |  | ||||       |  | |     ||    | | |  ||    ||  ||     || |  || |||    | || | || | ||   | ||||     |||||||||||||||| || || || ||||| |||||||| |||||||||||||| || || || || || ||||| ||||| |||||||||||||| || |
gtaatgtttccttttttccaaatctcgactctgttttctgaattaaagttagggtttttgaa-acgatctttggtttcttatgtggtgctttatctttttgtgtagGATATTGGAGGATGCGATATTCAGAAACAGGAAATTCGTGAGGCTGTTGAATTGCCTCTTACCCACCACGAGCTTTACAAACAGATTGGTATTGACCCAC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 1
--ctcacatatcctggagcttatttattattg-ctcactg-taatctattcatacagtcgacaaa-taaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
   |   || |  ||     | |||||| |   | || |  |||    ||       | | || | |   | ||| |   ||||||||    |  || || | ||||||||||||||||||| || || || || ||||| || || |||||||| |||||  |||| ||||||||||||||||| ||||||||||| |||||||
tatttgaatgtt-tgccatctttttattgtaaacacatttctaaatggttggggttctggtcagagtttgaaattcatggtttttttg----taccttttattagGATATTGGAGGATGTGATATTCAGAAGCAGGAAATCCGTGAAGCTGTTGAGTTACCTTTGACTCATCATGAGCTGTACAAACAGATTGGTATAGATCCTC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 1
----ctcacatatcctggagcttatttattattgctcactgtaatctattcatac-agtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
    ||     |||   |     || | || ||    | |||   | |||| ||| |||  |    |  |||| ||  ||| || | |  |     |   | ||||||||||| ||||| || || || |||||||||||  |||| ||||| ||  | || || |||||||| ||| | || ||||||||||||||||| || |
aaggcttgttcatct--gcatgaatctgttgttat--aatgtttgcaattcttacgagtgcagttttttaatacttt-catattgtcgaatggtggtggatgcagGATATTGGTGGATGCGATATTCAGAAACAAGAAATCAGGGAAGCTGTGGAGCTTCCACTTACACATCACGAGTTATATAAGCAGATTGGTATTGACCCAC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 1
---ctcacatatcctggagcttatttattat-tgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttt-tgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
      |    | | |        |||  |           || | || |  | |       | ||  | | || ||     ||  || |  ||| |     ||||||||||| |||||||| || ||||||||||| ||| | ||||| || ||  | || || ||||||||||| || |||||||||||||| || || || |
agaaaaatgatttccgttatagggttacgaagcagatgtcttagtttaattgttcccatt-tatatgcattgttcaaagcgattcgtgttcgtgagtg----cagGATATTGGTGGATGTGATATACAAAAACAAGAGATTAGAGAGGCCGTGGAGCTTCCACTTACACATCATGAACTATACAAGCAGATTGGCATCGACCCAC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 1
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
             |     |||| || || ||   ||  |     |       |||     |    |  | | || || |||  || |   |  ||||||||||||||||| ||||||||||| || |||||||| || ||||| || ||  | || ||||| || || ||||| ||||||||||||||||| ||||| |
-------------gtaagaattt-ttctttcttcttgcgactc--ttgagggctcgtgttcttgggt-ctaagcacttctttctttgt---ttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTATACAAGCAGATTGGTATCGATCCAC

upper sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ38338 (Selaginella moellendorffii), 3'ss of exon 1
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
            | |    ||||  | || || ||| |       || |    | |            | |||    || || |||     |  ||||||||||||||||| ||||||||||| || |||||||| || ||||| || ||  | || ||||| || || ||||| ||||||||||||||||| ||||| |
------------gtaagaaattt--tctttcttactcttgaaggctcgtgttcttgg----------gtctaaacacttcttacttt--gtttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC

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|58678900|gb|CK067587.1|CK067587
EST:     TCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: TCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|29656423|gb|CB652698.1|CB652698
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|13806060|gb|AU181330.1|AU181330
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|58673134|gb|CK061820.1|CK061820
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|14714069|gb|AU198009.1|AU198009
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|29659073|gb|CB655348.1|CB655348
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|29624298|gb|CB629309.1|CB629309
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|29628785|gb|CB633796.1|CB633796
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|29624228|gb|CB629239.1|CB629239
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|33801384|gb|CF326563.1|CF326563
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAA
EST: gi|11565135|gb|AU165771.1|AU165771
EST:     CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACG                         GATATTGGAGGAT-TGACATCC
genomic: CCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCC

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: 68 (upstream exon), 75 (downstream exon)
Score: 56

GCACCGCCACTCGAATGCGCTCGTCGACGTGCTGCCGCCCGAGGCGGACTCCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcagttttc ... ctattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC
                                       ttctgac  putative branch site (score: 56)
                                             ctattttc  CT-rich tract
           acaaataaaatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcacatatcctggagcttatttattattgctcactgtaatctattcatacagtcgacaaataaaatatttaacatttttttgcttctgactattttcagGATATTGGAGGATGTGACATCCAAAAACAAGAAATTCGGGAGGCTGTTGAATTACCGCTGACACATCATGAGCTGTACAAGCAGATTGGTATTGATCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - ctggagc
- - - - - - - - - - - - -tattgct
- - - - - - - - - - - - - - - - - - - - - - - catacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - cgacaaa