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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggccaaatgtttgttgtgtatttaattttcattgtctaattattattctaaaagttcaattttgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG

Basic information

species Zea mays
transcript GRMZM2G006507_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
----------gtagggccaaatgtttgttgtgtatttaattttcattgtctaattattattctaaaagttcaattttgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG
             || ||| |  ||| |||||||||||| |||| ||| | || |||   | | | | |||||||| ||||||||||||||||||||| |||||||| |||||||||||  |||||||||||||||| |||||||||||||||
gtaaggggctaagggcccagaattttattgtgtatttaaatttctttgcccaaatatctgtattaca-ttcaattt-gatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG

upper sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 10
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
----------------gtagggccaaatgtttgttgtgtatttaattttc-----attgtcta-attattattc--taaaagttcaattttg--atgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG
                       |  ||  |   | | |   |||  | |     | ||  || || | | |||  ||| || |   ||||   |  ||||| |||||||| ||||||||| | || || |||||| | |||||||| |||||||||||||||||||||
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG
















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|87153082|gb|DY397871.1|DY397871
EST:     GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGC                         ATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT
genomic: GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT
EST: gi|18964823|gb|BM661216.1|BM661216
EST:     GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGC                         ATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT
genomic: GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT
EST: gi|22490474|gb|BU050397.1|BU050397
EST:     GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGC                         ATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT
genomic: GAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGT

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 97

AGTAACTGAGGAGAGACCAGGCTGGTGCACTGATCCACATCTACCACCATGTGCAGCgtagggccaa ... tgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttaattttcattgtctaattattattctaaaagttcaattttgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG
     taattttcattgtcta  TA-rich tract