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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctctcttcttttgtaaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG

Basic information

species Oryza sativa
transcript LOC_Os10g42940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G011518_T01 (Zea mays), 3'ss of exon 3
----ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctctc--ttcttttgtaaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG
    ||| | ||||  | | ||| ||||| |||     ||    || ||   | |  |  ||| ||||   |||||  |  || |  || |||  | |||| |||||| ||||| |||||||| |||||||||||||| || ||||||||||| || || ||||||
tgatttatatatcctaggt-cttgatttattta-----cattgatttgtagtaaactctgtttccttgaaatgtaagatgttccccattatttgctgaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG

upper sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctct-cttcttttgtaaact---------cgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG
          || |   ||  |  || || |  |  ||||||  | |   |     ||||  |      | ||  ||||  | | | ||| |||            ||||||||| || ||||||||| ||||| ||||||||||||| | ||| |  || || ||||||
---------aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgta-acaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
















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|88764833|gb|CI773951.1|CI773951
EST:     AAATTGAGGCCCCTTATGGAGGCACTACTTCAACCACACCCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGA
genomic: AAATTGAGGCCC-TTATGGAGGCACTACTTCAACAACACC-GATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGA
EST: gi|88430649|gb|CI596763.1|CI596763
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGA
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGA
EST: gi|88738429|gb|CI761937.1|CI761937
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGA
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGA
EST: gi|29641419|gb|CB646426.1|CB646426
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|88765119|gb|CI774225.1|CI774225
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTG
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTG
EST: gi|66919127|gb|CX105975.1|CX105975
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|88405972|gb|CI591367.1|CI591367
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGA
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGA
EST: gi|88761917|gb|CI771473.1|CI771473
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|218479927|gb|FG968408.1|FG968408
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGA
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGA
EST: gi|33811779|gb|CF331776.1|CF331776
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAG
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAG
EST: gi|33795688|gb|CF323714.1|CF323714
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|218479871|gb|FG966995.1|FG966995
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|88743152|gb|CI766660.1|CI766660
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCT
EST: gi|88574643|gb|CI666412.1|CI666412
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTC
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTC
EST: gi|88426529|gb|CI579358.1|CI579358
EST:     AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTG                         ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGA
genomic: AAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactcttt ... aaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaaacacttttcttgcgttgtaaattcctctcttcttttgtaaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG
                            ttcctctcttcttttg  CT-rich tract
                     ttgtaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctctcttcttttgtaaactcgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA