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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagtaatactgtgctgcccatgaatattacccatgtcacaacaattgctttttaagtctattttgtcagaatgatgtgctcactgttttttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os12g44140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G129806_T01 (Zea mays), 3'ss of exon 7
caagtaatactgtgctgcccatgaatattacccatgtcacaacaattgctttttaagtctattttgtca--gaatgatgtgctcactgttttttctgtt------cagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG
        | ||  |   ||||| | |||   ||   ||     | |||||| |    |  |    |||  || | || || | |||  || || |||       ||||| || |||||||||||||||||||| ||||| |||||  || |||| || ||||| ||||| ||||||||||||||||| |||||||| ||||  ||||
--------attgcccgttccatgcaaattctgcaaaccatgtgcagtgctttattcaaccgtacaatcaaagagtaatttgattacttattattttgtatatctgcagGTCGCCAGTCAAGTAATCCACTGGCTCCATGATGAAGCGATGATTCTTGGGATGAACGTGACCAGAGATTTCCTGTGCCTGTACTTTGACCTTGGCCAAG

upper sequence: LOC_Os12g44140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G058004_T02 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------------caagtaatactgtgc--tgcc-----catgaatattacccatgtcacaacaattgctttttaagtctattttgtca--gaatgatgtgctcactgttttttctgtt------cagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG
                                                                  ||  |    ||| |  ||||     |||| | | |   ||   ||     | |||    |  |    | |   ||  ||||  | || | |||  || || |||       |||||||| || ||||||||||||||||| || || |||||  |||| || || ||||| | ||| | ||||||||||||||| ||||| || ||||| ||||
gtgattaaaactgcccacctcctcctttttttttgggtagatctcccaagcattatgcccctttgtaaaaacctttgtccattgccagttccatgcagagtctgcaaaccattttcagtgccacatgcgatcttctcaccaaagaatagtttgataacttgttattttgtgtatctgcagGTTGCCAGCCAAGTAATCCACTGGCTCCACGATGAAGCGGTGGTCCTTGGGATGAACGCGACAATAGATTTCCTGTGCCTGTACTTGGACCTTGACCAAG

upper sequence: LOC_Os12g44140.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0016g05020.t01 (Vitis vinifera), 3'ss of exon 7
ca-agtaatactgtgctgcccatgaatattacccatgtcacaacaattgctttttaagtctattttgtcagaa-tgatgtgctcactgttttttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG
|| | || |  ||   |  | |   |    | |||||            |      | |  |||   ||| || |||  |  | |  || || |     |||||||| |||||||| |||| |||||||||||| |||||  |     | || || || |  | | | || ||  | ||| | | ||||||  | || || |
catactagttttggagtagcaagagagcacatccatgg-gttgtgcccacagccacatttgattcattcataactgaatttattatggtcttctgcaa-cagGTTGCAAGTCAAGTTATCCGCTGGCTTCATGAGGAAGCTCTTAAGGTGGGAATAAAGGCAAATCGGGACTTTTTATGCTTGTCCTTTGAGATGGACCAGG

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|89188074|gb|CI115323.1|CI115323
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|38477155|gb|CF961288.1|CF961288
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86869799|gb|CI316527.1|CI316527
EST:     ATAGCTACAATTGTGACTT-GAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86255490|gb|CI065167.1|CI065167
EST:     CTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: CTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88505450|gb|CI432956.1|CI432956
EST:     CTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGG
genomic: CTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTC-GG
EST: gi|88476980|gb|CI414251.1|CI414251
EST:     CCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: CCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|58664911|gb|CK053597.1|CK053597
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86494399|gb|CI137032.1|CI137032
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88961835|gb|CI096988.1|CI096988
EST:     ATAGCTACAATTGTGACTTGGAGGACCCCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88476958|gb|CI414229.1|CI414229
EST:     AACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: AACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86851901|gb|CI316470.1|CI316470
EST:     ATAGCTACAATT-TGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86415025|gb|CI069428.1|CI069428
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88198711|gb|CI198561.1|CI198561
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86486823|gb|CI129456.1|CI129456
EST:     CCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: CCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88257877|gb|CI360463.1|CI360463
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|89177145|gb|CI043648.1|CI043648
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88273287|gb|CI388743.1|CI388743
EST:     CAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: CAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|87037454|gb|CI192076.1|CI192076
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCAGCTGGCTTCATGAAGAAGCATTGGTTCTCGG
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCA-CTGGCTTCATGAAGAAGCATTGGTTCTCGG
EST: gi|2798251|gb|AA751545.1|AA751545
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAANAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86432478|gb|CI086089.1|CI086089
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88519250|gb|CI446904.1|CI446904
EST:     CAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: CAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88508290|gb|CI435796.1|CI435796
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88235689|gb|CI234891.1|CI234891
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|88958290|gb|CI095809.1|CI095809
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|86436377|gb|CI118099.1|CI118099
EST:     ATAGCTACAATTGTGACTTGGGGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
EST: gi|218483279|gb|FG953413.1|FG953413
EST:     ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAG                         GTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT
genomic: ATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGT

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: 74 (upstream exon), 75 (downstream exon)
Score: 9

AAGCATTGCTGGATCATTGACTGGGAAGCCCTCCGATGGATATTTGGTAAATAGCTACAATTGTGACTTGGAGGACCTCCCAACAATGCTTCTGCAGCAGgtaaacttct ... ttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttttaagtctattttgtcagaatgatgtgctcactgttttttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG
                                tgctcac  putative branch site (score: 9)
                                  ctcactgttttttct  CT-rich tract
     ttttaagtctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagtaatactgtgctgcccatgaatattacccatgtcacaacaattgctttttaagtctattttgtcagaatgatgtgctcactgttttttctgttcagGTTGCTAGTCAAGTAATCCACTGGCTTCATGAAGAAGCATTGGTTCTCGGTATGAATGTGACTAGAGATTTCCTGTGCCTTTACTTTGATCTTGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - tgctgcc
- - - - - - - - - -catgaat
- - - - - - - - - - - - - - - -ccatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgtgc