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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG

Basic information

species Oryza sativa
transcript LOC_Os10g26600.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 3
gtaagcatcgtgt---tcataatatatttgtcatcaaattgaagcaaacactgcgat-ttatttcaggatgcatctggacctgacatgtttttt-tttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
||| ||||| |||   |  |  |  ||      |  | |  ||| | | |  | ||  ||| |    ||  |  | | | |  |||  ||   |  ||| |||||||||||||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||||
gtacgcatcatgtgtcttgttgttcatcctggctatagtgaaagtagagagggagacattagtctcagac-ctccagaagccaacaccttccatgcttgcagGTTGTTGAGATCACAAAGGGCAGTAAAGTGAAATATGAGCTAGACAAGAAGACCGGAATGATCAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
-gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgattta---tttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
  ||   || |  |  || | |        ||  ||||  |      | |   |||||   ||  || |      ||   |||     |   |   || ||||||| |||||||| || || ||||| || |||||||| |||||||||||||||||| |||| |||
tatagcaattgcatg-atgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 3
gtaagcatcgtgttcataat-atatttgtcatcaaattgaag-caaacactgcgatttatttcaggatgcatctggacctg-acatgttttttt-ttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
  |  || |   | ||| || | |     | || ||||  |  |      ||| ||| ||||     |  |   |    |   | ||||   |  ||||||||||| |||||||| || || ||||| || || ||||| |||||||||||||| ||| |||| |||
-catacagcaattgcatgatcacaccacacctctaattccattcttgagttgcaattaattttcttgtaaaggggagtttctgcttgttcaatggttgtagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAATATGAACTTGACAAGAAGACAGGATTGATTAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
||||      | | | | ||    |    |||  || |||  | |       |||| | |         | ||||  ||| ||           |||||| |||||||| |||||||||||||||| || ||||| |||||||| || || ||  | ||||||
gtaaagtctttatgcttgatgatgtgacaatccgatcgaaaaagagttaatcatttgtcttt-------tttgga--tgaaat-----------tagGTTATTGAGATCTCAAAGGGGAGCAAAGTCAAATATGAACTTGACAAAAAAACAGGTCTCATCAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
|||||  |    ||| || | |  ||||  || ||    || |     ||  |||   |||   |  ||| |   | |   ||| || ||     |||||||||||||||| || || ||||| || || || ||||||||||| ||||| ||| | ||||||
gtaagtttt---ttcctactct--ttgt--tctaaacagagta--tgttgttattagattctctaatcattttatctttggatgattatt-----agGTTGTTGAGATCACTAAAGGAAGCAAGGTCAAATACGAGCTTGACAAAAAGACAGGACTCATCAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgt-agGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
         || ||     |  | || | | | || | ||||   |  |    | | | ||    |   ||||     || |     | | | || |||| ||||||||||||||||| ||||||||||| ||||| || ||||| ||||| ||  | ||||||
---------gtattgtctcttaacttataacccaagt-aagccttctttaatctctctctctctcttggtctgttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
                   |||     ||||     |||  |  |  |  | ||||||||   |   |||         ||   |   ||  || ||||||||||||| || || || || ||||| |||||||||||||||||||| |||||  |||| |||
------------------gtatgcc-atcattcttctgattcttatccctc-atttattttctgt--cattcatcgtctac---tcccttggtgcagGTTGTTGAGATAACGAAAGGAAGTAAAGTTAAGTATGAGCTTGACAAGAAAACTGGGCTGATTAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
-gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgt---ttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG----------------------------------
    ||||  | ||| | | |||   |  |||| |         |  | |    ||| |   |        |||    |||  ||    |||  |    ||||| | |||||    ||||| |||||||||||||||||||| |||||||||| |||  ||||||||                                  
atctagcaatg-gttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagcatcgtgttcataatatatttgtcatcaaatt--gaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttt-----tgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
|   |    ||||  ||||| |      || || ||   | ||||    ||| || | |||| ||   |   | |    ||||| | ||          || ||||||| |||||||  |  |||||||| |||||||| ||||||||||||||||  ||  |||| |||
gcccgtggggtgtg-ataattt-cacagcagcatatcccgcagcacg-gctgggagtcattt-agatagtcacagtttatgacaaggttgagccacacgtgcagGTTGTCGAGATCAACAGAGGGAGCAAGGTGAAGTACGAGCTTGACAAGAAGAGCGGTCTGATGAAG

upper sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
         ||  |     |   || ||  | || |    |  | |       | |  ||  | | ||||     | |||   | ||||      |||| || || ||| | || || |||||||| ||||||||||| |||||| ||| |||| ||||||||
---------gttctggagctcccttagtttttaact--gcgtgagcttcatcctcttgtttggta-gCATT---GCTTGAATCGGTTTTCC----AGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG

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|32948243|gb|BP184815.1|BP184815
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|88389669|gb|CI603168.1|CI603168
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|88391448|gb|CI598266.1|CI598266
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|88314255|gb|CI602587.1|CI602587
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACA
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACA
EST: gi|88389431|gb|CI600600.1|CI600600
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|88405481|gb|CI588687.1|CI588687
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|12693435|gb|AU173568.1|AU173568
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|11564697|gb|AU165333.1|AU165333
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|11564695|gb|AU165331.1|AU165331
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
EST: gi|88404002|gb|CI601412.1|CI601412
EST:     GACCTGGAGCTCCTCAGGTTTTCAATGTT                         GTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG
genomic: GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAG

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: 63 (upstream exon), 66 (downstream exon)
Score: 15

GACCTGGAGCTCCTCAGGTTTTCAATGTTgtaagcatcg ... ttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
                                acctgac  putative branch site (score: 15)
                                        tgttttttttt  CT-rich tract
                                       atgtttttttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG