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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttggattcatttaagaaatttgagcagaatatcctctgcctctgggctagtgccttaacaatttggacttagcatgtgttgtagacttcattatgtaaatttctcgtgtgagtacataagcttgtttcacaatttctcgaggtgattttacataatcatgcttatcagtgtggtttgttttggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTAAGAGCTGACTAATCAAATATGGATCCTTTTCCTTTTGGTGAACAGCTGA

Basic information

species Oryza sativa
transcript LOC_Os03g22400.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22400.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G849959_T02 (Zea mays), 3'ss of exon 7
gtgagttggattcatttaagaaatttgagcagaatatcctc-tgcctctgggctagt-gccttaacaatttggac---ttagcatgtgttgtagacttcattatgtaaatttctcgtgtgagtacataagcttgtttcacaatttctcgaggtgattttacataatcatgcttatcagtgtggtttgttttggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTAAGAGCTGACTAATCAAATATGGATCCTTTTCCTTTTGGTGAACAG-CTGA
||| ||     |  || |  |||||| |||||| |   ||  || ||      ||    |   |||  |||  |    | |  |||  |  |  | ||    | |||   |   | ||||   || | |       ||    | | | |  ||||||   || ||| || | || |     |  ||||||     ||||||||| ||||||| ||||| || ||||| |||| || ||| ||||||||| |||||||||||| ||   |||   || | |  | ||||||   | || ||||
gtgggtgaacatgcttaataaaattttagcagactggactgatggctaaaacttaaccacgggaaccttttacatgcatgaagatgcttgttttagttatcaacgtagtataaccatgtgccgacctgaa---agatctgtctgttttggtgtgattaggcagaatgatacatacccaaaagaattgttt-atttctgcagGAACACATGGAGTATTTTAGGAAGAGGACAGCGAAGGAGATCTTAAGACTAAGAGCTGACTGAT-GGATAGACATTCATCACTTTTTGGAACAGAGGCTGA
















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|88902328|gb|CI374936.1|CI374936
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88478388|gb|CI415659.1|CI415659
EST:     TTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|89162394|gb|CI104722.1|CI104722
EST:     TTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88513377|gb|CI440883.1|CI440883
EST:     TTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88471999|gb|CI409270.1|CI409270
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|86833622|gb|CI337196.1|CI337196
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88281136|gb|CI402334.1|CI402334
EST:     AGGATTGAGCATTTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: AGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|86842207|gb|CI338528.1|CI338528
EST:     TCAAGTACATTGATTTCCACACCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|86432774|gb|CI086385.1|CI086385
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88263858|gb|CI367632.1|CI367632
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88254975|gb|CI353799.1|CI353799
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|29627374|gb|CB632385.1|CB632385
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88978221|gb|CI384697.1|CI384697
EST:     ACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: ACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88484068|gb|CI421339.1|CI421339
EST:     GAGCATTTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: GAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88514855|gb|CI442361.1|CI442361
EST:     GCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: GCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88903540|gb|CI089078.1|CI089078
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|87028902|gb|CI351205.1|CI351205
EST:     TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|88503707|gb|CI431213.1|CI431213
EST:     TGTCTTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
EST: gi|58594246|gb|CF992554.1|CF992554
EST:     TCAAGTACATTGATTTCCACAGCAGAGGACTGAGCATGTGGTTTAGTCAG                         GAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA
genomic: TCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTA

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), 22 (downstream exon)
Score: 5

GTGGGACTGTGGTATGTTTATGCTCAAGTACATTGATTTCCACAGCAGAGGATTGAGCATGTCTTTTAGTCAGgtgagttgga ... ggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTAAGAGCTGACTAATCAAATATGGATCCTTTTCCTTTTGGTGAACAGCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaggtgattttacataatcatgcttatcagtgtggtttgttttggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTAAGAGCTGACTAATCAAATATGGATCCTTTTCCTTTTGGTGAACAGCTGA
        attttacataatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttggattcatttaagaaatttgagcagaatatcctctgcctctgggctagtgccttaacaatttggacttagcatgtgttgtagacttcattatgtaaatttctcgtgtgagtacataagcttgtttcacaatttctcgaggtgattttacataatcatgcttatcagtgtggtttgttttggaactgcagGAAAACATGGAATATTTCAGAAAGAGAACAGTGATGGAAATCTTAAGATTAAGAGCTGACTAATCAAATATGGATCCTTTTCCTTTTGGTGAACAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA