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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAATTG

Basic information

species Oryza sativa
transcript LOC_Os01g51920.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 6
gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAAT-TG--
                          ||      ||     |||     | |  ||  || | || |   |||| ||  || ||   |  ||| || || |||||  |||||| ||||| || || |||||||||||||||||||||||||| |||||||||||||||||||| ||||| |   ||   ||  | ||||| || ||||  ||  
-------------------------gtgagcagctcacgcgtcat---gattccatccattccttataaaactg-aagtctctggcgtgttctaacttccatcttgcgcagGACCATGTTAACGACATTGACTTCGACTACAAGGAGTATGCGAGGCAGAGATTCGAGCAGTACTGGCACA---AGTCTGCGATCTTAACATCTTGAACATGTG

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G08600.2 (Glycine max), 3'ss of exon 6
-gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAATTG
  ||| || | |   |   |  |  |||   |  || |||||||| |   ||| ||    |   ||||||   ||  ||  |||         ||   | | | |  |||||  ||||||||||   |||||||| ||||||||||||||||| |||||||||||  |||| || |||  ||||||||   |  | ||    |||  || | 
gatattttaagagaccaaaa-atatattttattctttttttttcatagttactctaaaggttacttctgt--ttgctaatgtgt---------tgctttgtgtgtgttgcagAGTCATGTCAATACAATTGACTTTGACTACAAGGAGTATGCGAGGCAGAGATTTCAGCAATACTGGTTGAAGAAGCCTACTTTATTGGACTCACCAAGTA

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G74320.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGC--AAGCACTTTTAACTTCATGAATTG
                   |      | |     |||| | |||       ||  || ||   |||||  ||  || |   |    ||| ||        |   | | ||||| ||||| ||||| || ||||| ||||||| |||||||||||| || || |||||||||||||||   |  ||||  | || | ||  |  |   |||   
------------------gtaatttctacaatactcttctatca-------tacttgcatt--ttctga-accatatataggcttgattttcattttgtaaaactttacagGAACATGTGAATGAAATCGACTTTGACTACATGGAGTATGCAAGACAAAGGTTCGAGCAGTATTGGTTAACAAAGCCGAGGCTCCTTGCAGCTTCCGAAC--

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv13s0084g00150.t01 (Vitis vinifera), 3'ss of exon 7
gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCAT--GAATTG
           | | ||   | |   ||               | ||  | |  ||  |||| ||       |       |     ||| | |  | | | | || | ||||| ||||| ||||| ||||| ||| |||||| ||| |||||||||||||| || || || ||||||   | |||||  |  || ||   ||| |  | |   
-----------tatttgatggcctggtgtaaaagctagggaagagaattaatgcattcatcccttagaagtttcctggttttaatcattgtatctcttttctgtttttcagGAACATGTAAATGAAATTGATTTCAACTACATGGAATATGCAAGGCAGAGGTTTGAACAATATTGGTTAAGGAAGCCTGAGCTCTTGGGTTCTTCTGGAC--

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|38480982|gb|CF965071.1|CF965071
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|87037984|gb|CI192606.1|CI192606
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86497719|gb|CI140352.1|CI140352
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|58672419|gb|CK061105.1|CK061105
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATACTATCG                         GATCATGTCAATGATATTGACTTCGACTA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTA
EST: gi|89187600|gb|CI115046.1|CI115046
EST:     AATACACGCTCGCCAGTAATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86895302|gb|CI331230.1|CI331230
EST:     GAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGC-AGGCAGAGA
genomic: GAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86500529|gb|CI143162.1|CI143162
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|29634653|gb|CB639662.1|CB639662
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86495212|gb|CI137845.1|CI137845
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86828304|gb|CI276881.1|CI276881
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|89195521|gb|CI051634.1|CI051634
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86852839|gb|CI323148.1|CI323148
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGCCCTCTGGGGAATAATATCGG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAG
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATC-Ggtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAG
EST: gi|88975583|gb|CI021665.1|CI021665
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86851235|gb|CI312636.1|CI312636
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86496165|gb|CI138798.1|CI138798
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|87026021|gb|CI250037.1|CI250037
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|88223690|gb|CI223539.1|CI223539
EST:     TTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: TTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86499149|gb|CI141782.1|CI141782
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86500222|gb|CI142855.1|CI142855
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86436665|gb|CI118387.1|CI118387
EST:     ATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: ATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|33676050|gb|CF304289.1|CF304289
EST:     GGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: GGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|86499157|gb|CI141790.1|CI141790
EST:     AGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|88957209|gb|CI095195.1|CI095195
EST:     TAGTTTGGGGCCTCTGGGGAATAANATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: TAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|89162213|gb|CI104541.1|CI104541
EST:     TAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: TAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|33683158|gb|CF311397.1|CF311397
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|33676093|gb|CF304332.1|CF304332
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
EST: gi|87024609|gb|CI259324.1|CI259324
EST:     AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCG                         GATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA
genomic: AATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGA

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), 66 (downstream exon)
Score: 13

TGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTGAGAAATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAATATCGgtatgttcat ... tcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAATTG
                                 atctgac  putative branch site (score: 13)
                                       cctctatcttctgc  CT-rich tract
                             tattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcatatttctggatgtccattgcctgtttcttttttcaaaagaactatatgaatccattctgtcactgtaaacctgtgctattatctgacctctatcttctgcagGATCATGTCAATGATATTGACTTCGACTACAAGGAGTATGCAAGGCAGAGATTCGAGCAGTATTGGCAGAAGAAGCAAGCACTTTTAACTTCATGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG