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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcgcgcgcgcgcgcaatcctctctccctctcgctaactttccccatttttgcttttgcgttggctctcctcgttcgagtgggaacggaggcgcgtgtgcttgcgtgataagcttcgagctcgcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGCGGCGGCGTGCAGCCGCCGAACCTCCGCCCCACCCCGCCTACCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g58330.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58330.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G004356_T01 (Zea mays), 3'ss of exon 1
gtgagtgcgcgcgcgcgcgcaatcctctctccctctcgctaactttccccatttttgcttttgcgttggctctcctcgttcgagtgggaacggaggcgcgtgtgcttgcgtgataagcttcgagctcgcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGCGGCGGCGTGCAGCCGCCGAACCTCCGCCCCACCCCGCCTACCCAG
      | | |||| |   ||     | | |  || |  |  |||  |   |||| || |||||  | | |   |       |    || ||    |  | ||||| || || ||||||    ||||||||||| |||| |||||| |  | |||||| | || ||||||||||||| |||||||||||| |   ||||||| ||  |||||||| ||||||||||||| |||
------gtgagcgcccttccatcgtgcccgctttcccctttgcttcgc---ttttcgcctttgcacttgttgcacctaccaaac---gatcgcgtccctgagtgct-gcatgttaagctcttcgctcgcctctgcagGACCGGGAGGCTATACAGCTCCCTGGGCTCTTCCCGCCGGCGTTCGGCGGCGGTG---TGCAGCCACCCCACCTCCGCGCCACCCCGCCTACACAG
















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|29640714|gb|CB645723.1|CB645723
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
EST: gi|58591347|gb|CF989655.1|CF989655
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
EST: gi|58655984|gb|CK044664.1|CK044664
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
EST: gi|29679601|gb|CB675876.1|CB675876
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
EST: gi|87012603|gb|CI307351.1|CI307351
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCAAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGC
EST: gi|88447805|gb|CI577001.1|CI577001
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGAAGCAAGGGG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
EST: gi|58588059|gb|CF986367.1|CF986367
EST:     GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCG                         GATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC
genomic: GGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGC

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: 41 (upstream exon), 43 (downstream exon)
Score: 2

CCTCGCGCTCAGCCTCGACGCCGCCGCGGCGGCCGAGGCGTCCGGGAGCGGGAAGAGGCTCGGGGTCGGCGATGACGCCGAGGGTGGCGGCAGCAAGGCGgtgagtgcgc ... gcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGCGGCGGCGTGCAGCCGCCGAACCTCCGCCCCACCCCGCCTACCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgggaacggaggcgcgtgtgcttgcgtgataagcttcgagctcgcctctgtagGATCGGGAGACCGTGCAGCTCACCGGACTCTTCCCGCCGGTGTTCGGCGGCGGCGGCGTGCAGCCGCCGAACCTCCGCCCCACCCCGCCTACCCAG
                                          ctcgcctct  CT-rich tract