Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g12880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 2
--tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
  |   |  |  ||| |  ||   | |||  || |||       || |      | | |||  | ||  ||  |  |||    ||      |||| |||||| | ||||||||||  || || ||||||||||||||| | ||||||||||| ||||| |||||| | |||||||||||||||||||||||||||||||||
cataacttgtatttaataaggttttatatgatgattattctctatttcgttat-tatgaaaatattagcattgtc-tttcagatgacatctctctatttcagTTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 2
-tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
 |    |||   || ||| |  |||    || || |    ||  |  |     |   |||    ||  ||  |  ||  |  ||      || | |||||||| ||||||||||  || || || |||||||||||| | ||||||||||||||||| |||||| | |||||||| ||||||||||||||||||||||||
gtagaacatgtataattttgttatgatgatttttaaatttaatatttagctattgccaaaatgttagcattgtc-ttgctgatgatatctctatatttcagCTGTTGGAAACTGTTATAAAAAATTGTGGGGATATACTTCACATGCATGTTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 2
tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaata-atatcctgattttttttgg----gggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
    |    |  ||| |    | || |     | | || ||  |    |  ||||  ||| | |  | |  || |||| |||| |    |   ||| | ||| ||||  |||| ||    || ||||| |||||||| ||  |||||||||||||||| || ||||||||  | |||||||||||||| ||||| ||||| |||
----tacggaggattctatcta-gtctgcgtataaagaaaatgtctgtatcatctttaataattggaaaggctcatttgttttcgatttgactgctatattttagCTGCTGGAGACAATCATAAAGAATTGTGGGGACATTATCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G26440.2 (Glycine max), 3'ss of exon 2
------tgcttcattattattttggagatgtat--cttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
      ||| |  |   |  | || | ||   |  ||||| |||  ||  |||   | ||| | |||  |||  |    || |||| | | ||     | | ||  || | ||||| ||    || ||||||||||| |||||  | ||||||||||||||||||||||||||| | |||||||||||||| ||||| |||||||||
ctaagatgcattctctctgatctgcatataatttacttgtctagatca-tttg---atgatttgaaa--aat--tcatttggttttctgttggtccattgtattaaagTTGTTGGAGACAATCATAAAGAACTGTGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 2
tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataata-----tcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
         |  ||| ||   | || | |   | | || || ||    |  ||||  ||| | | | |        |  ||||   |  |   ||| | ||| ||||  |||| ||    || ||||| |||||||| ||  |||||||||||||||| || ||||||||  | |||||||||||||| ||||| ||||| |||
----cagggaggattctgtcta-gtctgtgtataaagaaaatttctgtatcatctttaataattgagaaagctcatttgttttccatttgactgctatattttagCTGCTGGAGACAATCATAAAGAATTGTGGGGACATTGTCCACATGCATGTTGCCGAGAGAGATGTTCTTCATGAGATGGTGAAAATAGTAAAGAAGAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 2
-------tgcttcattattattt-tggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
        | | |||| ||  |  || | |  |  |||||  ||  ||  |||   | ||| | |||  |||  |    || |||| | | ||   ||| | ||  || | ||||| ||    || |||||||| || |||||  | ||||||||||||||||||||||||||| | |||||||||||||| ||||| |||||||||
tcagctaggatgcattgtttctagtgtataattgacttgtccagatca-tttg---atgatttgaaa--aat--tcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 2
---tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
   |   |  |   | |  |  |      | |||  |    |  ||||| |   |||| | | ||  | ||   || ||||  ||  |     |||  |  |||| ||||| || |   | || |||||||| |||||  |||| |||||||| ||||| |||||| |  | |||||||||||||| ||||| |||||||||
ccttcagttgtagatttcattcaatcaattgttgcattctcctgcttgc-ctttatctgata-gaggattaaattggttttgcttttgtct-ttctactatagCTATTGGAGACAGTCGTAAAAAACTGTGGAGATATTGTCCATATGCATGTAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG

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|88694259|gb|CI738297.1|CI738297
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAAC
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAAC
EST: gi|88398026|gb|CI585529.1|CI585529
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88718071|gb|CI741581.1|CI741581
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTG
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTG
EST: gi|88404185|gb|CI575673.1|CI575673
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88744503|gb|CI767863.1|CI767863
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGG
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGG
EST: gi|58654984|gb|CK043664.1|CK043664
EST:     CAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: CAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|29674265|gb|CB670540.1|CB670540
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|86903843|gb|CI302489.1|CI302489
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACA
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACA
EST: gi|88299682|gb|CI577184.1|CI577184
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGG
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGG
EST: gi|88411131|gb|CI606350.1|CI606350
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88363396|gb|CI617957.1|CI617957
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88377286|gb|CI600441.1|CI600441
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|24208345|gb|AU225372.1|AU225372
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88761808|gb|CI771364.1|CI771364
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTT
EST: gi|88390599|gb|CI609224.1|CI609224
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATG
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATG
EST: gi|88371552|gb|CI602730.1|CI602730
EST:     AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACT                         CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCA
genomic: AGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCA

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: 73 (upstream exon), 75 (downstream exon)
Score: 44

GCAATCAAAAGATGTTGTTAAGGCACTCAAGAAAAGGATTGGGCACAAAAATCCAAAAGTCCAAATTCTTGCGCTGACTgtgagtttat ... tctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
                       tcctgat  putative branch site (score: 44)
                                            ctctgtttc  putative PPT
         taaaatgaataatatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttcattattattttggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
tgcttca
- - - - - - - - - - - - - - - - - - - - acttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgaa