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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttttaccatttctactcataacatttgagctggtatgtgaatgatgacattctaatggtagattacttgatttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG

Basic information

species Oryza sativa
transcript LOC_Os06g04270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 6
gtaagtcttttaccatttctactcataa-----catttga-gctggtatgtgaatgatgacattctaatggtagattacttgatttgtac--------agAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG
|||||  |     ||| |||||||| ||     |||||||  |||  |  || | ||| | | |||||||| |||||  |   ||| | |        |||||||||||||||||||||| | ||||||||||||||| || || ||||||||| | ||||| |||||||| ||||| ||||||||| | ||||| ||||
gtaagaata----catatctactcacaatactgcatttgatactgacacatggaggattaaactctaatggaagattcttgtctttttccccttctctagAAATACACTCCAGAGAGCCCAGGAGATGCCACCAGGAACCTCTCCCAGCAGTGCCTGAACGCCCTTGCTAATGTTGTGCCTGGTCTTATCGGAGGCAGTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 6
-gtaagtctt--ttaccatttctactc----ataacatttgagct--ggtatgtgaatgatgacattctaatggtagatt-acttgatttgtac----agAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG
  | | || |  |  | |||| | ||     |||| | ||||  |     || |   |   ||   |  |||       | | |||||||  ||    ||| |||||||||||| |||||||| ||||| || || |||||||| |||||     |||| || |||| ||| ||| |||||||||| ||||| || ||||
cttcactcatcatccctatttttgcttcatgataaaacttgacttccatcatttatttctggattattgaatacccttctgatttgatttcaactttcagACATACACTCCAGAAAGCCCTGCTGATGCTACAAGAAATCTGTCTCAGCAAAATCTAAATGCCCTTGTTAAGGTTCTTCCTGGTCTACTTGGTGGCAGTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------------------gtaagtcttttaccatttctactcataacatttgagctggtatgtgaatgatgacattctaatggtaga---ttactt--gatttg--tacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG
                                                                          ||||   | |  |||||   |        | |    ||  |   ||   | |  | | |||  || |   |  |||   |||||  | |||| |||||||||||||||||| || ||||||||||| || ||||| ||      | | || || ||||| || ||| |||| ||||| ||||| || ||||
gtgagtaaattctaaactcacaggtttttcttacatgtttgtaacttttcaaggtttggattacatactatccaaagttgatcatgatttcagtttgatttggtagtatggggcttcaaaaagttat-tccaaatattaaaacctggcttccaatttgatttcagACATACACTCCAGAGAGCCCAGCGGATGCCACCAGAAACCTGTCTCAAACAAACCTTAATGCCCTTGCAAAGGTTCTTCCCGGTCTGCTTGGTGGCAGTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtcttttaccatttctactcataacatttgagctggtatgtgaatgatgacattctaatggtagattacttgatttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG
||||||      |  |||  | ||   ||| || |  ||||||   |   ||||  |    |   |   |   ||   || |  ||| |||||| ||||||   || |  ||||||||||| || ||||||||||| ||  | ||||| ||||||||||||||||| ||| | ||||| |||||||
gtaagtagaactctctttgcattctgtacaattcaattggtattctagatatgagttatagaacatctttctttttccttttttagACATACACACCAGAGTCTCCAGGTGATGCCACCAGAAACCTGTCACAGCAATGTCTTAACGCCCTTGCTAAAGTTGTTCCCGGTTTCCTTGGTGGAAGTG

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|33679471|gb|CF307710.1|CF307710
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|33380946|gb|CF196289.1|CF196289
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29618033|gb|CB623045.1|CB623045
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58655034|gb|CK043714.1|CK043714
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29616475|gb|CB621487.1|CB621487
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|33381554|gb|CF196897.1|CF196897
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29687957|gb|CB684232.1|CB684232
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58693256|gb|CK081943.1|CK081943
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29629389|gb|CB634398.1|CB634398
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|33794200|gb|CF322990.1|CF322990
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58694523|gb|CK083210.1|CK083210
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|700946|gb|D47237.1|D47237
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGNTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGGATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58691917|gb|CK080604.1|CK080604
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29621963|gb|CB626974.1|CB626974
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29617346|gb|CB622358.1|CB622358
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29656978|gb|CB653253.1|CB653253
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58611032|gb|CK038744.1|CK038744
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGA
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGA
EST: gi|29615703|gb|CB620715.1|CB620715
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58612671|gb|CK040383.1|CK040383
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|33381650|gb|CF196993.1|CF196993
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGNNAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|33681879|gb|CF310118.1|CF310118
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58656118|gb|CK044798.1|CK044798
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29686071|gb|CB682346.1|CB682346
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29677194|gb|CB673469.1|CB673469
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29614136|gb|CB619149.1|CB619149
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58689877|gb|CK078564.1|CK078564
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|29642621|gb|CB647628.1|CB647628
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
EST: gi|58609714|gb|CK037747.1|CK037747
EST:     AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCT                         AAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG
genomic: AGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAG

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: 68 (upstream exon), 66 (downstream exon)
Score: 102

TAAGTTCGCCGAGTATGAGAAGAAGTACCCAGAAGATGCAGCGACCTTGAAGAGCATTGTCTCAGGGGAGTTGCCTGCTGGCTGGGCTGACGCTCTTCCTgtaagtcttt ... atttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagctggtatgtgaatgatgacattctaatggtagattacttgatttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG
                        attctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttttaccatttctactcataacatttgagctggtatgtgaatgatgacattctaatggtagattacttgatttgtacagAAATACACTCCAGAGAGCCCTGCAGATGCCACCAGGAATCTGTCACAGCAGTGCTTAAACGCACTTGCTAAAGTTGTTCCTGGTCTTCTTGGAGGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA