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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttccacacttttttttcaattgttttcatctgccttgcctgcctttagaaacttccaatgagttataaactgtttgctctttctcctggcattttctgttgctttcatag

Basic information

species Oryza sativa
transcript LOC_Os03g44900.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44900.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G100246_T01 (Zea mays), 5'ss of exon 4
AATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttccacacttttttttcaattgttttcatctgccttgcctgcctttagaaacttccaatgagttataaactgtttgctctttctcctggcattttctgttgctttcatag
| |||||||| |  | ||||| |||||  |||||||||||||||| ||| ||||  ||||| |||| ||  || |||||||||| |||||||| || || || ||||| |     | |||   | || | || || |      ||||||       ||  ||  ||| || | | | ||| | | || ||| |  || | |   |  ||||   ||
AGTTCAGGCATCAATTGTATCGAATCCCACCTTTTGGGAAAGAATTGGTAGCGACACATTAGCTACCGACATGCTGTTCTTTGCGTTCTACTACCAACAGgtcaattttccttgctctttccaatttatatttattt------cctgcc-------accaccggtgaattttcatcagttagtttttactcgtaacaatgttctt--cttttgcag
















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|88662190|gb|CI466119.1|CI466119
EST:     TTTGCTTTTTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: TTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|89195186|gb|CI051299.1|CI051299
EST:     GCGATTCATNATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|89178711|gb|CI391709.1|CI391709
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|86522596|gb|CI162802.1|CI162802
EST:     GCGATTCATGATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|29630459|gb|CB635468.1|CB635468
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88663021|gb|CI477176.1|CI477176
EST:     TACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: TACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|8527420|gb|AU092235.1|AU092235
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88268296|gb|CI378231.1|CI378231
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88469340|gb|CI406611.1|CI406611
EST:     TACTATCAGCCA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: TACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88275469|gb|CI395320.1|CI395320
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88524842|gb|CI453795.1|CI453795
EST:     TGTTCTTTGCTTTTTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: TGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|88663563|gb|CI483262.1|CI483262
EST:     ACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: ACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|33812923|gb|CF332349.1|CF332349
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|29676310|gb|CB672585.1|CB672585
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|4715388|gb|AU056505.1|AU056505
EST:     CGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTG
genomic: CGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTAT-CAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTG
EST: gi|29667066|gb|CB663341.1|CB663341
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
EST: gi|218487618|gb|FG950215.1|FG950215
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACT
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACT
EST: gi|86840245|gb|CI342475.1|CI342475
EST:     GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAA                         AACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG
genomic: GCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGG

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: 64 (upstream exon), 74 (downstream exon)
Score: 61

AATTCAGGCACCTGTAGTATCAAATCCTGCCTTTTGGGAAAGAATGGGTGGCGATTCATTATCTACGGATTTGTTGTTCTTTGCTTTCTACTATCAGCAAgtaaatttcc ... gctttcatagAACACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGAAGCAATCGTGGAGATTTCACAGAAAGTACAATACTTGGTTCCAACGGCACGTGGAGCCAC




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