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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaagaaaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG

Basic information

species Oryza sativa
transcript LOC_Os05g02310.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
--gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaaga--aaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG
  | | || |  | |||    |   |    |    ||     ||   | |   |||      | |||  || | | |  | | ||| | |   ||   || |||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||   |
ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcatagaa-gcgactcctat---tcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
--gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaagaaaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG
    |  | ||   | |   |||   ||||  |                  |  ||||    | |||  || |  |||||     || |||   |||| |||||  | || ||    |  || |||||||| ||||||||||||||||| | ||||||||| ||  ||
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatac-ttgtgaaatattgctgaatcttg-cagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG

upper sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 3
gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaagaaaagagaggaaaaactctaacaaattgtgtct---cttttctgtcacttgt-cagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG
 || ||     | |||  || ||   ||  |  |  ||  |  | ||     |       || |    |    |  | | |   | | | | | | || | |||||  |||| ||    |  || |||||||| ||||||||||||||||||||||||||||||||   |
actagtg----aaatttgacaaaattttcataaataaattgttagaaaccttgccttcttaatcaaccaaggttcttatttgaacatatgtctaatttttgcagGTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

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|88381548|gb|CI682205.1|CI682205
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88720264|gb|CI743563.1|CI743563
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|4878573|gb|AU062872.1|AU062872
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88725059|gb|CI748318.1|CI748318
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|58598649|gb|CK009177.1|CK009177
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88396360|gb|CI598472.1|CI598472
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|33663512|gb|CF294479.1|CF294479
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|699797|gb|D46088.1|D46088
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagG-TCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAA
EST: gi|86831354|gb|CI297623.1|CI297623
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGA
EST: gi|88300593|gb|CI587397.1|CI587397
EST:     GACCTGGTGCAC-AACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATA
EST: gi|88400835|gb|CI616840.1|CI616840
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88425227|gb|CI564744.1|CI564744
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88300279|gb|CI584698.1|CI584698
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|117243396|gb|CT843443.1|CT843443
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|3759881|gb|C97139.1|C97139
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGGTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88578597|gb|CI687538.1|CI687538
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|88325992|gb|CI651039.1|CI651039
EST:     GACCTGGTGCACCAACTATATTCAACTGC                         GTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA

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: 75 (upstream exon), 66 (downstream exon)
Score: 38

GACCTGGTGCACCAACTATATTCAACTGCgtaaggccac ... cacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaaaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG
                  ctctaac  putative branch site (score: 38)
                                 tctcttttctgtcact  putative PPT
                     taacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaagaaaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - acaccaa
- - - - - - - - - - - - - - - - gaccaaa
- - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - -gaaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa