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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagcagtagaaactggagacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g28200.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G162672_T01 (Zea mays), 5'ss of exon 14
TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagcagtagaaactggagacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcag
||||| |||||||| |||||||||||||||||||| |||||||| |||||| ||||| | | | |||| | | ||  | |   |||||   ||   ||     || ||   |  |  |||  ||    |   |  |    ||   | ||  |  |                        
TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAGgtgtgcttcagctgg-ttctcccactctcttactacttccgatccagctccagctcttcc---ctttctaaa--ggtcttaggtagtgtttggtt-ccggagtatgg------------------------

upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G18470.1 (Glycine max), 5'ss of exon 14
TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagc-agtagaaactggagacaaccaacgc-----acagtcatctgatcagtgc-aatcttacatttgccaaatgcag
||| | || |||||||||||||||||||| ||||| || ||||| ||||| |     | ||  |  ||| |||| |              |   ||   |||   |||||   || |    |    |||||  |   |     | ||| |  |  ||    | |||   ||| | |     |||||
TTCAAGTATTTCCTCAAGGACCCTGTGAAATATGATGTTAAATATCAGgtaca----tattgac--cttaaatttagcttctaagcataacaaaatggagaagtggccaaatgagcaatgccctatgacaatgacatctttttagagtaaattattctaaactaattgaacactcgt-gtttgcag

upper sequence: LOC_Os05g28200.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G51820.1 (Arabidopsis thaliana), 5'ss of exon 13
TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttctgttagcttcttcaattcattcatctcttccttccccat-tctgaaa---ctgccaagcagtagaaactggagacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcag
||  ||||||| |||||||||||||| || || |||||||| ||||||||  |      | | |||  |  |    ||  | |  |  |     || | ||| |   ||   || ||| ||   || || |||  || |       ||                                   
TTTAAATACTTTCTCAAGGACCCTGTCAAATACGACGTCAAGTACCAGgtaag------tcaacttagtacacatgtttgtgttcttttgaaatatctttgagaggtctcttaatcagaagttgcttgaaacactcatcttgattacag----------------------------------

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|38481364|gb|CF965453.1|CF965453
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|27547699|gb|CA765724.2|CA765724
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88967759|gb|CI098001.1|CI098001
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86540861|gb|CI181067.1|CI181067
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86419098|gb|CI053899.1|CI053899
EST:     TGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86494917|gb|CI137550.1|CI137550
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTTTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88967555|gb|CI014906.1|CI014906
EST:     GTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|89167777|gb|CI021476.1|CI021476
EST:     GTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|89176415|gb|CI043436.1|CI043436
EST:     TGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88975033|gb|CI023284.1|CI023284
EST:     AGTTCCGATACTTCCTCAAGGAGCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: AGTTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88962890|gb|CI025376.1|CI025376
EST:     TGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|3763399|gb|AU030151.1|AU030151
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|313079556|gb|HO213114.1|HO213114
EST:     GTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA

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: 48 (upstream exon), 70 (downstream exon)
Score: 19

TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCAACCAGCCACTGATGAAAGCAGCAATCGCCCTGGACTGTGATTCTGTGAC




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