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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgaaggccgaatgcagttgagcacacagcttcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG

Basic information

species Zea mays
transcript GRMZM2G080375_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 10
---------------------------gtaagtcg--aaggccgaatgcagttgagcacacagcttcttgaacatggcttgttctga-aaccttgatg--ggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
                            | | ||   |  |   | | ||||| ||  |    |  |    |     | | | |||| || || ||    |  | ||   |  || | | ||||| ||||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
gtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgatt-tctacagAGAATCACGGAGAAGCAGAACAAGGTGGTGATCACGGACAGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCATGCTTCCTGAGCCACGAGGACG

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtcgaagg-ccgaatgcagttgagcacacagcttcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtt-tgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
|| ||||  ||| || ||| |   |       || ||  |  |          ||  | || | | ||     || | |    | || || |||||||||| ||||| |||||||||||||||||||| ||| | |||||||||||| |  |||  ||||||||||| ||  | ||| |||  || |  ||| 
gtgagtctcaggaccaaatactcatacctgagcatctcttacatttatatcaatttgggaatcctaataa--catggtttgaatattgtgtagAGGATCACGGAGAAACAGAACAAGGTGGTGATCACTGACAGAATGTGGGCGAGGCTTTTGTCTTCGACGAACCAACCGAGTTTCATGAAGCAAGCTGACA

upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 10
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtaa-gtcgaaggccg--aatgcagttgagcacacagcttcttgaacatggc--ttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
     ||  |||    |     |   | ||| |   ||          | |||     |  |  |   || || |||   |    || | |   || |||||||| || ||||| |||||| | ||||||||||| ||| |||||||||| ||| | || |  ||||| ||||||||  | ||| || ||| | | || |
catcatactgtcatcagttatcatcaccgttaaagtcatcatcctcatatcatcataatcatagtatcacttttatgtaaacatcatttttatgttacagAGGATAACGGAGAAACAGAACCATGTGGTGATCACAGACAGGATGTGGGCAAGGCTACTCTCTTCGACAAACCAGCCGAGTTTCTTGGGCCCCAAAGATG

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|74234372|gb|DT642286.1|DT642286
EST:     GCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTTTAT                         AGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG
genomic: GCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTCTATgtaagtcgaa ... ttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCG




















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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 27

CACTCTGCTGGCCCACAGCGCCCTCCATGGCGCCATGGCGGGGTACACCGGCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTCTATgtaagtcgaa ... ttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


Block sizes: 47 (upstream exon), 34 (downstream exon)
Score: 19

CACTCTGCTGGCCCACAGCGCCCTCCATGGCGCCATGGCGGGGTACACCGGCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTCTATgtaagtcgaa ... ttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 17

CACTCTGCTGGCCCACAGCGCCCTCCATGGCGCCATGGCGGGGTACACCGGCTTCACGGTCGCTCCGGTCAACGGCAGGCACGCCTACATCCCGTTCTATgtaagtcgaa ... ttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgaacatggcttgttctgaaaccttgatgggcaatcgatctcttgtttgcagAGGATCACCGAGAAGCAGAACAAGGTGGTGATCACGGACCGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCCTGCTTCCTGAGCCACGAGGACG
                        ccttgat  putative branch site (score: 17)
                                         tctcttgttt  putative PPT