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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgacgttaaatcgtagtatttgtgatgtatttttgtggttttatttcaaacaaataattggacttgttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG

Basic information

species Oryza sativa
transcript LOC_Os08g44810.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 7
gtacttgacgtt-aaatcgtagtatttgtgatgt----attttt----gtggttttatttcaaacaaata-attggacttgttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG
||   |||| || |||   || ||| | |  |      |||  |    |       |  | || |||  | |    |  |  ||||||||||||||||||||||| ||||||||||||||||||||||||||  ||||||||||||||||||| || || ||||||
gtgactgaccttgaaactttattatgtctcctcctcccattcctaacaggaaaaacagattaagcaatcacacacaatctcctttttgtagCTGGCACTAAAAGCAGGTGTATTTTATGACAAAGTATCAAACGTGACTATTTGGGGGAACCATTCGACGACTCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT5G58330.3 (Arabidopsis thaliana), 3'ss of exon 5
gtacttgacgttaaatcgtagtatttgtgatgtatttttgtggttttatttcaaacaaataattgg--acttgttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG
||||| ||  | | | |    ||| ||||||   | | ||   | |  || || ||| || ||||   | ||   |||||||||| || || ||||| ||||| || ||||||||||| || |||||||| || ||||| || ||||| || ||||||
gtactagatttcacacc----tatatgtgat---tgtatgcaatatatttgcatacatatgattgacaatttccattttgtagCTTGCTCTTAAAGCCGGTGTTTTCTATGACAAAGTGTCTAATATGACCATATGGGGAAATCACTCCACGACTCAG

upper sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtacttga---cgttaaatcgtagtatttgtgatgtatttttgtggttttatttcaaacaaat-aattggacttgttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG
                    ||| | |   | | | |  ||  | ||| | ||| |     |    |  ||         || |||| ||  || ||| || ||||||| || ||||| ||||| || ||||| ||||| |||||| | || ||||||||||| ||||| || ||||||
gttaagtagcttgtgaccattacctcagtccatgatacagtcatgtttattatgaacaaaaggaaatcaataattgttgtatgaattcgatgtgatttgtgcagCTGGCTCTCAAAGCAGGTGTCTTCTATGATAAAGTGTCAAATGTAACCATTTGGGGGAATCACTCGACCACTCAG

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|84117267|gb|CD151034.1|CD151034
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAACCAAGTGCCAG                         CTGGCACTAAAAGCGGGTGTATTTTATGAC
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGAC
EST: gi|38468692|gb|CF952823.1|CF952823
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG                         CTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
EST: gi|29686259|gb|CB682534.1|CB682534
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGATAATAGAGCCAAGTGCCAG                         CTGGCACTATAAGCGGGTGTATTCTATGACAAAGTATCA
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCA
EST: gi|29613418|gb|CB618431.1|CB618431
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG                         CTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
EST: gi|29677718|gb|CB673993.1|CB673993
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG                         CTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
EST: gi|29686257|gb|CB682532.1|CB682532
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG                         CTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTA
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTA
EST: gi|29677717|gb|CB673992.1|CB673992
EST:     AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAG                         CTGGCACTANAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT
genomic: AAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATT

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), 71 (downstream exon)
Score: 42

TGCATTGATTTGCTTAAAGAATGCTCCCAACATACCAGCAAAAAACTTTCATGCATTGACGAGGTTGGATGAAAATAGAGCCAAGTGCCAGgtacttgacg ... ttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgtatttttgtggttttatttcaaacaaataattggacttgttttttgtagCTGGCACTAAAAGCGGGTGTATTTTATGACAAAGTATCAAATATGACTATTTGGGGGAACCACTCAACAACTCAG
                                         cttgtttttt  CT-rich tract
                 ttttatttcaaacaaa  TA-rich tract