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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactactgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC

Basic information

species Oryza sativa
transcript LOC_Os10g33720.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 7
-ttactact--gattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatt-tgtatat-gcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
 || | |    ||||||   | || | |  |||  |       |  ||  ||  |   | |    | | | |||||  ||||||||| |||  ||  | | ||||||||||||| ||||||||||||||||||||||| ||||||||||| |||||| ||||||| ||||||||||| || ||||| ||||| || ||||| || 
tttgcaatcaagattgtcattattggca-ggtttccgtagaagcgggaacatcgt---gcttccacatttataattc-actcaaatccaataatgcgttttgcagGTGTGAAGCCTTCTCAACCTATCCTCGAACATACGATCTTCTCCACGCATGGGCAGTCTTTTCTGACCTTGATAAAAGAGGCTGCAGTGCCGAAGACCTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G107629_T05 (Zea mays), 3'ss of exon 3
-----ttactactgatt-gtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
     ||| || ||    |||| ||        |  | ||||   || || ||  || | | | | ||   ||  |  |  | |  ||| |  ||    | |||||||||||||| ||||| ||||||||||||||||||||||||||||| |||||| |||||||||| ||||| || || ||||| ||||| || ||||| || 
gattgttattattggcgagtttctgcagaagcggggaacaac--atcgtgcttccac-atgtaca-gtttactcaagatacaat--aatgtgtttgcactttgcagGTGTGAAGCCTTCTCGACCTATCCTCGAACATATGATCTTCTCCACGCATGGGCAGTCTTCTCCGACCTCGATAAAAGAGGCTGCAGTGCTGAAGACCTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 6
ttactactgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctc--tgtaattttactcaaatctaatttgtatatg-cagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
   | | |||  ||  |   |  ||||  |||  |     |||  | |   |     |||  |||   ||| |  ||       | |    |  || || ||||||||||||||| || ||||| ||||| || |||||| | ||||||||||||||  | || |||||  ||    ||| ||  |||||  |||| ||| | 
--cccattgaaagtgcg-actgtgatatatatttaagccacatcgtcactgttgaagtattaccttcttgtgaccttggcttgttttggcatcaatgtgacagGTGTGAAGCATTTTCGACCTACCCTCGTACTTATGATTTGCTCCATGCATGGACTATATTTTCTGATATTATTGAGAAAGAGTGCAGTCCAGAGGATTTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 6
ttactactgattgtttgtgtttggatagt-tatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatat--gcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
    |  |  || |   || || | ||     | || |  ||    |   || |    | | |    | ||| || |      | |   ||  ||     ||||||||||||||| |||||||| |||||||| || ||||| |||||||||||||| || || |||||  ||   |||| ||  |||||  |||| ||| | 
---tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 7
ttactactgattgtttgtgtttggat--agttatcaacttgtcatgattatactaaggatatgtcctctgtaatttta----ctcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
    | || |||  | |  | | |||  |||| | |  || |  |  || ||         ||     ||  |   ||     |   || | ||     ||  ||||||||||||||| ||||| || || || ||||| ||| | || ||||||||||| |||||||||||| | || || | |||||||||   ||| ||||| 
----tgcttatt-ctagaatctagatttagttgttagatt-ttgtttttgtagctcctccgtgaatgatgagaaaataagagttttgatgtgataatcttaaacagGTGTGAAGCATTTTCAACATACCCCCGGACATACGATTTACTTCATGCATGGACTGTCTTCTCTGACATAGAAAATAAAGGTTGCAGTAAAGAGGATCTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 7
ttactactgattgtttgtgtttggatagttatcaacttgt-catgattatactaaggatatgtcctctgtaat-tttactcaa--atctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
    || |  | | |  |  ||| || |||   ||        ||| |||      ||| || |    || || |||||| ||  |   ||  | | |   ||||||||||||||  ||||| || || || || |||||| | |||||||||||||| || || |||||| |||| | |||||| |||||  |||| ||||| 
---ttattagtagctcctccttgtattgttcagaatcaaaatctgagtatggatgtgat-tgacaaaagtgatatttactgaaggaatgaacatcttttaacagGTGTGAAGCATATTCAACATACCCCCGGACTTATGATTTACTCCATGCATGGACTGTGTTTTCTGACATTGAAACGAGAGGGTGCAGTCCAGAGGATCTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 6
--ttactactgattgtttgtgtt--tggatagttatcaacttgtcatgattatactaaggatatgtcctc--tgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
    |   | || ||   ||| |    |||| | || ||     | |  || |  |     |||| |||   ||| || ||  |        ||   | ||  ||||||||||||||| || ||||| ||||| || |||||||| ||||||||||||||  | || |||||  ||    |||  |  |||||  |||| ||| | 
caagatacccgaatgaaagtgctacctgata-taattaaacca-cgtctttgttgttgcagtatgaccttgttgtgatcttgttttggc---atcaatgta-acagGTGTGAAGCATTTTCGACCTACCCTCGTACTTATGATCTGCTCCATGCATGGACTATATTTTCTGATATTATTGAGAAGGAGTGCAGTCCAGAGGATTTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 7
---ttactactgattgtttgt---gtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
   ||  || ||| || ||         |   | |  ||||| |   || |   |  || |    | |  ||  | || |||  || ||  |   ||      |||||||||||| || |||||||| |||||||| |||||||| |||||||||||||| || || |||||  ||   |||| ||  |||||  |||| ||| | 
gtttttttaatgaatgattagtaaacacgtgaaatcttcaacgttgaattacctttttatgaccttata-tcaatgatgttatgcatataaatgctg-----acagGTGTGAAGCTTTTTCAACCTACCCTCGAACGTATGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 7
ttactactgattgtttgtgtttggatagtt--atcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
       | | | ||| |  ||  ||  |   |   ||   | ||   || ||  |   |      | |   || ||  | ||        ||||    |||||||||||||||||| || |||||  | ||||||||||| |||||||| |||    |  | || ||  |  | || | ||| || || | ||  ||| | 
------gtcagtttttatacttaaattttcgaaatgacacattatttctacaccgaatttgaaatttttagcatgtttttgaa--------tgtac-cacagGTGTGAAGCATTCTCGACATATCCAAGGACATATGATCTCCTCCATGCTTGGGATATTATATCGGATATCAAGAAAAAAGGATGTAGTGAAGTGGATTTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 7
ttactactgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaa-atctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
| | ||   |   |  |  |   |  |   |  || |||  |      |  | | |   |      || ||||  | | |     | |||| | |  ||||||||||||| ||||| || |||||||| || |||||| | ||||| || ||||| || ||||||||| |||| |||| ||| || || || || ||||| 
tgattataaaccatgaggatggtgtgaaaaagaaaattgaaactgaagt-ttgatgtggtagatattgaaattcaattgactggatgatttcttttggcagGTGTGAAGCTTTCTCGACTTATCCTCGGACTTATGATTTACTCCACGCTTGGACTGTTTTCTCTGACATTGAAAAGAAAGGCTGTAGTGCTGAGGATCTG

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 6
--ttactac-----tgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
  |||  |       ||   ||| | || |  | || |   | |  || |    | |  || || ||  |    | |  ||    ||   | | | ||      |||||||||||| ||||||||||| || ||||| || || || |||||||| ||||| |||||||||||  | ||    |  || || || ||||| ||| | 
cattataaaaggcacgaccatttcttttagagttgtaaa-gattgttcttttccagatcaatga-atcactgaaggatcttcttgcatgccaactctg-----acagGTGTGAAGCCTTCTCAACCTACCCACGAACCTACGACCTACTCCATGCCTGGACCGTCTTCTCTGATATAGAGCGAAATGGGTGTAGTGCAGAGGATTTA

upper sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S322_38V6.1 (Physcomitrella patens), 3'ss of exon 6
-ttactactgattgtttgtgtttggatagttatcaacttgtc-atgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
   |   ||      ||   | |    ||||| | ||||  | ||  || |  |     ||| |  | | ||||   || ||  | |  ||||  | |||||||| |||||||| ||||| ||||| |||||||||||  | |||||||| || |  || || || ||  |  ||||    | ||||||| |   ||| || 
tacatagctatcaactttgatcttcccagttagctacttccccattttttttatttttttattttttttttaatca-acgcagcttttgtttg-gtttgcagGTGCGAAGCATTTTCAACTTATCCACGAACATATGACTTGCTCCATGCCTGTAATGTGTTATCGGATGTCTACAACCATGATTGCAGCTCTATAGACCTG

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|58688720|gb|CK077407.1|CK077407
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|86827969|gb|CI274889.1|CI274889
EST:     TCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: TCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|87039140|gb|CI193762.1|CI193762
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|25802153|gb|CA758114.1|CA758114
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCNCATGCAT
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTC-CATGCAT
EST: gi|87039008|gb|CI193630.1|CI193630
EST:     CTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: CTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|58694554|gb|CK083241.1|CK083241
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|58696008|gb|CK084695.1|CK084695
EST:     TAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: TAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
EST: gi|163921630|gb|EG714156.1|EG714156
EST:     ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTG                         GTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG
genomic: ACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATG

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: 71 (upstream exon), 45 (downstream exon)
Score: 23

AGGAAAAGGATGTATGGGTCATGAATGTTGTTCCACATGATGGACCAAGCACTCTCAAGATAATCTATGACAGAGGGCTTATAGGTTCTACTCATGACTGgtatgtgtca ... gtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
                                    atctaat  putative branch site (score: 23)
                       taattttactcaaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactactgattgtttgtgtttggatagttatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatatgcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG