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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA

Basic information

species Oryza sativa
transcript LOC_Os01g49000.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 1
----------------------------------------------------------aaagctactatcatcataga-agtactatgtcatcat-ttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA
                                                            |     |  ||  |||   |  | | | ||||  |  |||| || |  |     |  | ||||   ||||||||||| | | ||| || |  | | |||| || || || || |||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| || |||||||| ||||| || |||
gtatgtggagttaattttcctagatgttgctcgtgtctacaagtcaatgaaaaattcctcaatattttgcactataagcaagaatgtatcattctgctagacaacagaaaatgtacctatatgt-ttaatgtatttatccattttctttcttaatatcagTGCCTCCGGCGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCA

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------aaagct----actatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA
                                                         ||   |    || || | |||  | |||  ||          |  ||| | | |  | | ||     || ||||||||||  | | |||||  | |  | ||||||| |||||||| |||||||| ||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| || ||||||||||||||||| |||
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccataagcatgaatgtatcattctgctggacaagaaaaaatgtacctatat-cgccagttaatgtatttgtccatttttt--ctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 2
------aaagctactatcatcatagaagtactatg--tcatcattt-agaaaatactat----gaccagatgtatgagctaatgt-----attta--ccaagttttttaccaactttca---gAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
       || || || || |||| |      ||||  ||||| | | |  || || |||    ||  |  | ||| | ||          ||| |  ||   || || |     |||||   | |||||||| |||||||| ||||| || ||||||||||||||||||||||||||  | || ||||||||||||||||| || | |||||||||| | ||  
gtaagtcaatcttct-tcttcatggggcatgtatgcttcatcttctcaccaagtaatattagggataatttttatcaactgtcacgaaagattgaaccctgattgttgagtttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGCTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGC

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
    | |   || || ||     |       |   ||||  || |   | ||    | | |||| | | ||  |      |||| |||         ||| |||||||| |||||||| ||||| || ||||| ||||||||||||||||||||  | || ||||||||||||||||| || | |||||||||| | ||  
--gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacga----aagaatgaacca-tgattcagttgagttctttttt--tcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGT

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 4
-aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactt-tcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
      |||      | |     |  |  ||   | ||||     || |||  |  |  || |  | | |  |  | |   | ||   |   |  |  |||| ||||||||||||||||| || || || ||||||||||||||||||||||||||  | || |||||||  |||||| | || | ||| |||||| | ||  
tgcttgtacatgttccttgattctgttgggttcacttttaatttgtattatctcttgtagt-tatgttgagat-ctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAGGATGGT-AGCCGT

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 4
aaagctactatcatcatagaa-gtactatgtcatcatttagaaaatactatgacc-----agatgta--tgagctaatgtatttaccaagttttttaccaactt-tcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
        |||  || |||   ||  |  ||   | ||||     || |||  |      || ||||  |  | | |  |  | |   | ||   |   |  |  |||| ||||||||||||||||| || || || ||||||||||||||||||||||||||  | || |||||||  |||||| | || | |||||||||| | ||  
--------tatgttcctaggctgtgttgggttcacttttaatttgtattatctcttgtagagttgtagttatgttgagat-ctgattgaattcacttttacttaatcagGGCTTCTGGTGAGCATGAATCGTCCAGAAGGGTGAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAGCAATAGTGCCACAAATGAAGATGGT-AGCCGT

upper sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 4
aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgta--tgagctaatgtatttaccaagttttt-taccaacttt----cagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA
      | | |  |  | ||   | | ||   | |||   || ||||| |    || |     |    |  |||      ||| | |   || || | ||    ||| ||||| || |||||||| || || ||  ||||||||||||||||||| |||||  | || |||||||| || ||||||||   ||||||||||   | |
------aatgttgtggttgagaaaatgtgaacttatt-gtaagatacttttggtagtttctcttatattggtgttaaactcaaatatgaataacatcgtttgtccagGGCTTCAGGGGAGCATGAATCTTCCAGACGGGTGAAGTCTGAACTTCTGGTTCAGGTTGATGGTGTAAACAACAGTTCTACAGGTGAAGATGGTAGTCGA

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|58694007|gb|CK082694.1|CK082694
EST:     CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGG                         AGCTTCTGGTGAGCATGAGTCAT
genomic: CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGGgtatgtgaat ... caactttcagAGCTTCTGGTGAGCATGAGTCAT
EST: gi|58607003|gb|CK035036.1|CK035036
EST:     CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGG                         AGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT
genomic: CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGGgtatgtgaat ... caactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT
EST: gi|29625418|gb|CB630429.1|CB630429
EST:     CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGG                         AGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT
genomic: CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGGgtatgtgaat ... caactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT
EST: gi|29638398|gb|CB643407.1|CB643407
EST:     CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGG                         AGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT
genomic: CCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGGgtatgtgaat ... caactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGT

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: 49 (upstream exon), 73 (downstream exon)
Score: 14

AGAGTGAGCGCATGGTCCGCTGTTTATTTGATCTTGCAAGGTTCTATGCTCCAAGTACAATCTTCATTGATGAAATTGACTCCCTCTGCACATCTCGTGGgtatgtgaat ... caactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA
                  agctaat  putative branch site (score: 14)
                                     ttttttacc  putative PPT
                     taatgtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- agctact
- - - - - - - - - - - - - - - - - - - agaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctaatg