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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatttacaaattttatttttaagtggttaaccttatggagatgtgtaattctaactttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g40620.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G086052_T03 (Zea mays), 3'ss of exon 7
gtaggatttacaaattttatttttaagtggttaaccttatggagatgtgtaattctaactttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT
||| | ||||||   | | ||| |       ||||| || ||| | ||||||| || |||||| ||||||||||| |||||| | ||||| || || |||||||||||| | | |||  ||||||| || ||||||||||| || ||||| ||||||||  ||||||| 
gtaagctttacaggctatgtttatgtaattgtaaccgtaaggaaacgtgtaatgcttactttgcagcagGTTTCGGTTTGTTTTGTCTCCCCATCCCACAGCCTCTTTAATCTACCTCGCCAAGCGTTGTGGTTGGGCTAGCTCCGAGGAGCTTGAGAAGATTGAGCAC

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G082026_T01 (Zea mays), 3'ss of exon 1
gtaggatttacaaattttatttttaagtggtt--aaccttatggagatgtgtaattctaactttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT
||| | ||||||||  | |  |||| ||  ||  |||| || ||| ||||||||| || |||||| ||||||||||| |||||||||||||| || || |||||||||||| ||| |||  ||||| | || |||||||| || || ||||| ||||||||  |||| |||
gtaagctttacaaaagtcacgtttatgtacttttaaccgtaaggaaatgtgtaatgcttactttgcagcagGTTTCGGTTTGTTCTATCTCCCCATCCCACAGCCTCTTTAATTTACCTCGCCAAGTGTTGTGGTTGGGCAAGCTCCGAGGAGCTTGAGAAGATTGATCAT

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G28700.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------gtaggatttacaaattttatttttaagtggttaaccttatggag--atgtgtaattctaactttgtag---cagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT
               |  |   | |||    || | | |||  |     ||    |   |||  || || |    |||| |    ||||| |||||||||||||| |||||||||||| |  |     | |  ||    || || |||   |||||||   ||||||||   |||||| | || |||
gtaagtatcagggaaatcaaagaaaaaggagatatatcagtcttgggatttgcaaaatcatgaatagttgttgtgttgttggtttagGTTCCGCTTTGTTCTATCCCCACAGCCTACACCTGCAGCCTTGTATCTCATGAAACGTTGCACATGGGCTACACCTGAGGAAAGGGAGAAAATGGAACAT

upper sequence: LOC_Os01g40620.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0066g02600.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------gtaggatttacaaattttatttttaagtggttaaccttatgg-agatgtgtaattctaactttgtag--cagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT
                                           |     ||     ||||  |||  |    || ||  | ||  || | | |  ||  |  | | | |   |||||||| |||||||||||||||||| ||||| |  |   ||| |   |     | || |||   |||||| |  |||| ||| | |  ||  |||| || 
gtaagcttttgggactgcagtctgtcagaatttgtttgtttgttttttctttttttttttgctttagaaaattttactatttgataggttttttttttcacatatattggttagGTTTCGTTTTGTTCTATCTCCACAGTCTACACCTGCAAAACTCTATTTGATGGAACGTTGCAAGTGGGCTGGGGCTGAAGAAATAGCAAAGCTTGATCAG

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|25800535|gb|CA756496.1|CA756496
EST:     GCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC                         GTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTC
genomic: GCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATCgtaggattta ... tttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTC
EST: gi|29644655|gb|CB649662.1|CB649662
EST:     GCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATC                         GTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTC
genomic: GCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATCgtaggattta ... tttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTC

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: 53 (upstream exon), 72 (downstream exon)
Score: 13

AAAGCATCACGTGGCTGGTGCGAGAAGATGGTGGATCTTGCAGAAGACTCATCgtaggattta ... tttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttttaagtggttaaccttatggagatgtgtaattctaactttgtagcagGTTTCGCTTTGTTCTATCTCCACAGCCTACAGCCTCTTTACTTTTCCTTTCCAAGCGGTGCGGTTGGGCTAGTTCTGAGGAACTTGAGAAAGTTGAGCAT
                                      ttctaac  putative branch site (score: 13)
     tttttaagt  TA-rich tract