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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcagctaaccgtgtttctatgcttgggataatgttctttcgcccccctttttgttttctcttgtcctctgttgtaatgcaatcaattttgtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT

Basic information

species Oryza sativa
transcript LOC_Os06g45710.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 2
-agcagctaaccgtgtttctatgcttgggataatgttctttcgcccccctttttgttttctcttgtcctctgttgtaat---gcaatcaattttgtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT
 || || || |  |  ||||||   |  ||  |||    |  |       |  ||  |  |  || | |     || ||   ||  | | | |  | ||||||||| || |||||||||||||| || || ||||| |||||||||||||| ||  |  ||||| | ||||||||  |||| 
gaggagtta-ctattattctat---taagaccatgaatgtcagaaaagtgtggtgagtagtagtgacttgaaaagtgattttgccttgactatgctgttttcagGGACGTCCAAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCAAGGCTGTCTCAACTTCTTGGAATTGAG

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 2
agcagctaaccgtgtttctatgcttggg-ataatgttctttcgccccccttt---ttgttttctcttgtcctctgttgtaatgcaatcaattttgtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT
      | |      || |    |||||  || |  |  |         |||   | ||| |  ||||     ||  ||  |||  | | | |  | ||||||||| || || ||||||||||| || || ||||| |||||||||||||| ||  |  ||||| | ||||| ||  |||| 
--ttttttatttaacttttgcttttgggtgtattagttatagagtgtgatttgagtggttgtgacttgaaaaatg--gttttgccttgactatgctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCAAGGCTGTCTCAACTTCTCGGAATTGAG

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
agcagctaaccgtgtttctatgcttgggataatgttctttcgccccccttt--ttgttttctcttgtcctctgttgtaatgcaatcaattttgtctt----ttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT
      |||  || ||  || | ||      || |  ||   | |   ||   |||  |  |  |||    |      ||| |    || |    ||    ||||||| |||||||||||||| || || ||||||||||| ||||||||||| ||  | |||||||| |||||||||||||| 
------taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG

upper sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 1
agcagctaaccgtgtttctatgcttgggataatgttctttcgcccccctt--tttgttttctcttgtcctctgttgtaatgcaatcaatt-----ttgtc-ttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT
            ||||||| | | ||   |  | |   |||    |      | | ||||  ||||| ||   || | |  |     |||     ||||| ||||||||| |||||||| ||||| || || |||||||||||||| |||||||| ||  |  ||||||| |||||||| ||||| 
-------gtttttgtttct-ttcctgactttctatggattcatttcttggaatatatttttacttgttctaatttatgaaactgatgattctgaattgtcgttttcagGGGCGCCCAAAGGGTGTTACACCTAAGTACAGCTTGAAACCTCTTGTGCCAAGGCTGTCTGAACTTCTTGGAGTTGAG

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|58589338|gb|CF987646.1|CF987646
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|33658427|gb|CF281040.1|CF281040
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACNCCCGAAGTACAGCTTGAAGCCTCTTGTTCC
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAAC-CCCGAAGTACAGCTTGAAGCCTCTTGTTCC
EST: gi|58677408|gb|CK066095.1|CK066095
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|58668078|gb|CK056764.1|CK056764
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88313529|gb|CI671652.1|CI671652
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88327337|gb|CI645117.1|CI645117
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88392654|gb|CI625476.1|CI625476
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|29675440|gb|CB671715.1|CB671715
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88393098|gb|CI616582.1|CI616582
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|33677818|gb|CF306057.1|CF306057
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCTTTC-TCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGTTTCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|33813054|gb|CF332417.1|CF332417
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|33688490|gb|CF316729.1|CF316729
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|58689757|gb|CK078444.1|CK078444
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88332298|gb|CI656167.1|CI656167
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|86849751|gb|CI301639.1|CI301639
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88325004|gb|CI645019.1|CI645019
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88353244|gb|CI654510.1|CI654510
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
EST: gi|88338304|gb|CI655493.1|CI655493
EST:     TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTG                         GGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG
genomic: TCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCG

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: 74 (upstream exon), 75 (downstream exon)
Score: 30

CAGCCAGAAGATCACCGACGACACCCGCATCCGCGCGTCGGTTCCCACCATCAAGTTCTTGATGGGGAAGGGCGCCAAGGTCATCCTGGCCAGCCATCTGgtgaggatta ... gtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctttttgttttctcttgtcctctgttgtaatgcaatcaattttgtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT
                                         ttttgtcttttc  CT-rich tract
                                   aatcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcagctaaccgtgtttctatgcttgggataatgttctttcgcccccctttttgttttctcttgtcctctgttgtaatgcaatcaattttgtcttttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
agcagct
- - - - - - tgtttct
- - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - tgttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcaa