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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttagacctcactacaaaatagagatcctgaattctaattctgttaggtag

Basic information

species Oryza sativa
transcript LOC_Os01g68010.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068392_T02 (Zea mays), 5'ss of exon 3
GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttaga-cctcactacaaaatagagatcctgaattctaattctgttaggtag----
 ||||||||| |||| | ||| ||  | ||||||||||||||| ||||||||||||||   |||||||| || || ||||| || |||||||  ||||||||| | | || || |||||| |     || |    ||| ||||||| | ||||  | | ||| |    |    ||       |  |  | |   |  || | || | |||| |   ||||||||| | |||||| || | | || |||||||    
ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcat--acctatggtatcttgattgcagttttt-gttgcacatatatt----tacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtaggtag

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 3
GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttaga-cctcactacaaaatagagatcctgaattctaattctgttaggtag
 ||||||||| |||| | ||| ||  | ||||||||||||||| ||||||||||||||   |||||||| || || ||||| || |||||||  ||||||||| | | || || |||||| |     || |    ||| ||||||| | ||||  | | ||| |    |    ||       |  |  | |   |  || | || | |||| |   ||||||||| | |||||| || | | || |||||||
ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcat--acctatggtatcttgattgcagttttt-gttgcacatatatt----tacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctaggtag

upper sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068392_T04 (Zea mays), 5'ss of exon 2
GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttaga-cctcactacaaaatagagatcctgaattctaattctgttaggtag
 ||||||||| |||| | ||| ||  | ||||||||||||||| ||||||||||||||   |||||||| || || ||||| || |||||||  ||||||||| | | || || |||||| |     || |    ||| ||||||| | ||||  | | ||| |    |    ||       |  |  | |   |  || | || | |||| |   ||||||||| | |||||| || | | || |||    
ACTGGGCTATCTGCCCAATGACCGCTCGCTGTGGGAGCAGGAGCTGGCAAAGAAGAGAGGGCAGTACGCTGCTTTCAAAGATGAGTTCCTTACAAACCCTgtaagtcgctgcacattcaggtcat--acctatggtatcttgattgcagttttt-gttgcacatatatt----tacctagtttatggccaccaatgcctggctaaatcctctcccgaaaatagaggttctgaatcctgaatttgctag----

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|88336570|gb|CI656841.1|CI656841
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCA
EST: gi|88339196|gb|CI633767.1|CI633767
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGGA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|38565749|gb|CK085202.1|CK085202
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88742952|gb|CI766460.1|CI766460
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88370350|gb|CI587740.1|CI587740
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88341320|gb|CI640077.1|CI640077
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|9866162|gb|AU101912.1|AU101912
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88364426|gb|CI644504.1|CI644504
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|88737467|gb|CI759348.1|CI759348
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         G
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtag-
EST: gi|58652950|gb|CK041630.1|CK041630
EST:     AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCT                         ATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA
genomic: AGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCA

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: 42 (upstream exon), 57 (downstream exon)
Score: 4

GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgcccct ... tgttaggtagATGGAAATTGCACGGCAACGGGAATTAGAAGGCCAAGGGAGTGAGAATGCAGGGAGTATATATAATGGGTTACTTCATAGATCAGAGGTTACACAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGCTATTTGCCGAGTGATCGTGCCCTGTGGGAGCAGGAGTTGGCAAAGAAGAGATCACAGTACGCAGCCTTTAAAGAAGAATTCCTTAGCAACCCTgtatgccccttcagattcagatttgtgactttctctattttgattgtaattttaagatacacgtgcggtgtagtatagtacctgagatccctttttgcttgttagacctcactacaaaatagagatcctgaattctaattctgttaggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG