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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA

Basic information

species Oryza sativa
transcript LOC_Os03g18590.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G029543_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------gcgcacattctaa-----aaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
                                                                       || ||| ||      |  | |||     || |||  |          | |    |||   ||    | |  | |   |    | | | |||| | || |||||| ||||||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || ||||  || ||||| | |||||| |
gtcggtgttcccacaatgttttgcttgagccatatttgtggaattattatctataattttatatggttaaccatattttagttttcagttcttatgtcccattttcctttttgtttcaatcttagtatgc-taccaaaggaatttacatt---gttaatcattgtatttccagGTTCGCCTAGCTGTTGCTGGCGCTTTCCATACTAGCTTCATGCAACCAGCTGTTTCAAGATTGGAATCTGCGTTGGCTGCCACTGAGATTAGAACACCTA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G053639_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------gcgcacattctaaaaatattagacagcaattt---tttacaaacacatagcaagatatatgtaa-atgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
                                                                          ||  || |  | | ||  || |  |    ||| | |     |  ||   |   | |   | ||   |  |||   || | | |||||| | || |||||| || |||||| ||||||||||||| ||||| |||||||||||||| |||||||||||| ||||| |||| |||||||  || || || | |||||| |
gttagtgttccaaaaatgttttacttgaagcatatttatggaaatatatcatctataattttatatggctaggaatattacagctttcagttagtatgtcccattttccattttgtttcattcttagtattttacgaaaagaatttacatg-gttaaccattgtatttccagGTTCGGCTAGCTCTTGCTGGTGCTTTGCATACTAGCTTCATGCAACCAGCTGTTTCAAGACTGGAACCTGCGTTAGCTGCTACTGAAATTAGAACACCTA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA11G29520.1 (Glycine max), 3'ss of exon 4
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatg-tgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
             |    || | |   ||| || ||    |  ||  ||   |   |  ||   ||  || |||||           | |     |  ||||||| |||||||||||||||||||||||| || || || ||| |||| ||||| ||||| |||||| | ||||| ||    ||||| || | ||| ||||
-----------gtatgactttgcccctaatcttctattttccaatgccacctttcctcaaagaaataatgcctttg-----------cttctctgtggcagGTGCACCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGAAACCAGCTGTGTCAAGGTTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G06500.1 (Glycine max), 3'ss of exon 7
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatg-tgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
              | ||||   |  ||||||| ||    |  ||  ||   |   |  ||   ||  || |||||           | |     |  |||||||||||||||||||||||||||||||| || || || ||| |||| ||||| |||||||||||| | ||||| ||    ||||| || | ||| ||||
------------gtattattttgcc-caattttctattttccaatgccacctttcctcaaagaaataatgcctttg-----------cttctctgtggcagGTGCGCCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGGAACCAGCTGTGTCAAGATTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA11G29490.1 (Glycine max), 3'ss of exon 7
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatg-tgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
             |    || | |   ||| || ||    |  ||  ||   |   |  ||   ||  || |||||           | |     |  |||||||||||||||||||||||||||||||| || || || ||| |||| ||||| ||||| |||||| | ||||| ||    ||||| || | ||| ||||
-----------gtatgactttgcccctaatcttctattttccaatgccacctttcctcaaagaaataatgcctttg-----------cttctctgtggcagGTGCGCCTAGCTGTTGCTGGTGCTTTCCACACTAGTTTTATGAAACCAGCTGTGTCAAGGTTGGAAGCAGCATTGGCAACAACAGAAATCAGAACCCCAA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G30200.2 (Arabidopsis thaliana), 3'ss of exon 7
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatgt-gtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
                |||    |      |  || ||   |  |    | || |   |  ||| | |        |    | || |  ||   |    ||||||| ||||||||||| ||||||||||| || || |||||| |||| || || || ||||| ||| ||||||| || |  |||||||| | ||  || |
---------------gtatcct-ctctctctaattccatttatgttatgaaatcttcctcgatgctatcagaaacatgattgttggcggttggttctgtagGTGCGTCTAGCTGTTGCAGGTGCTTTCCACACTAGTTTCATGGAACCAGCAGTCTCGAGATTAGAAGCTGCATTGGCAGCCACAGAGATCAGAAGTCCGA

upper sequence: LOC_Os03g18590.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv06s0004g07380.t01 (Vitis vinifera), 3'ss of exon 7
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
               || ||      || |||| |      |   | |     |   | ||      || |      |          || ||||  |||||||| || || || |||||||||||||| ||    |||||| |||||||||| |||||||||||| |  || | || |  || || || | ||| ||||
-------------gtatttttctttacagttttctgtctgaagccatccttccaccagcaagactcatggcacaactt--------ttttctcttctcagGTGCGTCTTGCAGTGGCTGGTGCTTTCCACACTCATTTCATGGAACCTGCTGTCTCAAGATTGGAAGCCACACTGGCAGCTACGGAAATCAGAACTCCAA

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|86434605|gb|CI105838.1|CI105838
EST:     GCCAAAGCAAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
genomic: GCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
EST: gi|29678025|gb|CB674300.1|CB674300
EST:     GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
genomic: GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
EST: gi|88974541|gb|CI022082.1|CI022082
EST:     GGATTGAAGCAGTCGAAGCCCAAGCCAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
genomic: GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
EST: gi|58677960|gb|CK066647.1|CK066647
EST:     GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAAC
genomic: GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAAC
EST: gi|88962243|gb|CI097396.1|CI097396
EST:     CGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
genomic: CGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
EST: gi|25800454|gb|CA756415.1|CA756415
EST:     GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGCTTTCCATACNAGCTTCATGCAACCTGCT
genomic: GGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCT
EST: gi|86827662|gb|CI272928.1|CI272928
EST:     TTTAAGGCCAGAATGACG                         GTGCGCCTAGCTGTTGCTGGTGGCTTTCCATACAAGCTTCATGCAACCTGC
genomic: TTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGT-GCTTTCCATACAAGCTTCATGCAACCTGC

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: 59 (upstream exon), 67 (downstream exon)
Score: 30

GGGAACTATGCAGTTTCTGGTGGTGTGAAGGGGATTGAAGCAGTCGAAGCCAAAGCAAAGTCCTTTAAGGCCAGAATGACGgttagtgttc ... atcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaagatatatgtaaatgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA
                                           ttatctt  CT-rich tract
      atatatgtaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgcacattctaaaaatattagacagcaattttttacaaacacatagcaagatatatgtaaatgatgtgtctttgtctgcggtgaccattatcttaccagGTGCGCCTAGCTGTTGCTGGTGCTTTCCATACAAGCTTCATGCAACCTGCTGTTTCAAGATTGGAATCTGCATTAGCTGAGACAGAGATAAAAACACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- -cacattc
- - - - - -aaaaata
- - - - - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - -agcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - -atatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgatgt