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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcaagttcttcaatttcatgcctttttctgcatccaacaaagcttagatttcagctaaattaagctcctagctgacgagttcttgaaacttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT

Basic information

species Oryza sativa
transcript LOC_Os10g36690.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36690.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G114570_T01 (Zea mays), 3'ss of exon 1
-------gctcaagttcttcaatttcatgcctttttctgcatccaacaaagcttagatttcagctaaattaagctcctagctgacga-gttcttgaaacttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT
        |   |  |||   || |       ||  |||| |    | |   ||||||   |  ||||||  | |   | || || | ||||||| |||| |||| | ||||||| || || || || || || || |||||||||||||| || ||||||||||||||||| || || ||||||||||| || |||||||||||   
ccatctaccctgaactctgagatgttcctgagttggctgcctttctcca---ttagatca-aattaaattctgttggcaccttactatgttcttggaact-gcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG---
















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|88357414|gb|CI622263.1|CI622263
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88393181|gb|CI616665.1|CI616665
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88360326|gb|CI612045.1|CI612045
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88373226|gb|CI614562.1|CI614562
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|29631350|gb|CB636359.1|CB636359
EST:     CTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
genomic: CTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
EST: gi|88430721|gb|CI596835.1|CI596835
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88359741|gb|CI622431.1|CI622431
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|87008887|gb|CI304830.1|CI304830
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
EST: gi|88728439|gb|CI751949.1|CI751949
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88729904|gb|CI753125.1|CI753125
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|58666274|gb|CK054960.1|CK054960
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
EST: gi|88722812|gb|CI746322.1|CI746322
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88739395|gb|CI762903.1|CI762903
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88396558|gb|CI601041.1|CI601041
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
EST: gi|88345044|gb|CI625890.1|CI625890
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88763962|gb|CI773378.1|CI773378
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88744794|gb|CI768154.1|CI768154
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88404254|gb|CI575742.1|CI575742
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88692658|gb|CI736233.1|CI736233
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|29679560|gb|CB675835.1|CB675835
EST:     GAGGGGTCTCCT-TTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GAGGGGTCT-CTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88721479|gb|CI744778.1|CI744778
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88390160|gb|CI605613.1|CI605613
EST:     GGAGGGGTCTCTGGTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88343158|gb|CI627118.1|CI627118
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|58667856|gb|CK056542.1|CK056542
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88740934|gb|CI763449.1|CI763449
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88421613|gb|CI618737.1|CI618737
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88315101|gb|CI611765.1|CI611765
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88732660|gb|CI755837.1|CI755837
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|88357492|gb|CI623546.1|CI623546
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGCAG                       
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACT--A-CAGgtccgtagtt ... cttgcagc
EST: gi|88718719|gb|CI742229.1|CI742229
EST:     GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCACCACCTGCAAG
genomic: GGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagC--C-ATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAG
EST: gi|29634800|gb|CB639809.1|CB639809
EST:     CTTTCTTCCTGAGCTGGCTTCTTTACTACAG                         CCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT
genomic: CTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAAT

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: 43 (upstream exon), 39 (downstream exon)
Score: 2

GCTGCTGCTCCTCTCCTCTCCCTCTCAGCCTCTGGAGGAGGAAGAGAAGAGGAGGGGTCTCTGCTTCATCTTTCTTCCTGAGCTGGCTTCTTTACTACAGgtccgtagtt ... cttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatttcagctaaattaagctcctagctgacgagttcttgaaacttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT
                          agctgac  putative branch site (score: 2)
            taaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcaagttcttcaatttcatgcctttttctgcatccaacaaagcttagatttcagctaaattaagctcctagctgacgagttcttgaaacttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - ttcatgc
- - - - - - - - - - - - - - - tgcatcc
- - - - - - - - - - - - - - - - - - -aacaaag
- - - - - - - - - - - - - - - - - - - - - - - - - -ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcttg