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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttccaattatatcgctatattcatctctgtaatgtttaattatatgttaaaaacacacatataggtttctgtgactattgcttaatagtttgaaggcaatgtatgtcaaagtatctacacctaatgtttcttccattgaaggttcttgttatggttattacttggcacttacatcaattgcaattttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG

Basic information

species Zea mays
transcript GRMZM2G095868_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g17540.3 (Oryza sativa), 3'ss of exon 7
gtatgttttccaattatat---cgctatattcatc--tctgtaatgttt--aattatatgttaaaaacacacatataggtttctg-tgactattgcttaatagtttgaaggcaatgtatgtcaaagtatctacacctaatgtttcttccattgaaggttcttgttatggt-tattacttggcacttacatcaattgcaattttctt-cagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG-------
|| ||| || |||| ||||     ||| | |  ||  | ||||   ||    |||  |  |||     | | | | | | | ||| | |   ||   || |   |||||        ||||  |  |  ||  |  |  |    |    | || |    |||  | |||| ||| |||  | ||||||||||||| |||   |||| |||| || |||||||||||| ||| |||||| |||| ||||||||||||||||||||| ||||| |||||| ||||||||||||||||||||||||       
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaa--------atgttgagatgactttatttgtttgaacacataatgtatcaactt--tgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTGGTCAGGT

upper sequence: GRMZM2G095868_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g17540.1 (Oryza sativa), 3'ss of exon 9
gtatgttttccaattatatcg---ctatattcatc--tctgtaatgttta--attatatgttaaaaacacacatata-ggtttctgtgactattgcttaatagtttgaaggcaatgtatgtcaaagtatctacacctaatgtttcttccattgaaggttcttgttatggt-tattacttggcacttacatcaattgcaattttctt-cagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG
|| ||| || |||| ||||     ||| | |  ||  | ||||   ||    |||  |  |||     | | | | | |||    || |   ||   || |   |||||        ||||  |  |  ||  |  |  |    |    | || |    |||  | |||| ||| |||  | ||||||||||||| |||   |||| |||| || |||||||||||| ||| |||||| |||| ||||||||||||||||||||| ||||| |||||| ||||||||||||||||||||||||
gtttgtatttcaatgatattattactacacttgtccttttgtagcattctgcatttcacattatcttaaaaaaaacatggtcctggtcatgcttttgtattcagttgaa--------atgttgagatgactttatttgtttgaacacataatgtatcaactt--tgtggtgtatcactctgtacttacatcaattacaaccctctttcagCAAAGCATATGGATTTCCTGGGAGTTCAGGTGGCATGGGTGACTGGACCATGGTTTCTTTCAATTTTCATCAATATGCTTCCATGGGAAAGTG
















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: 47 (upstream exon), 46 (downstream exon)
Score: 16

GTTGACCAACTCGTCCTTGAGGAGGTTGTACGAGAAAGGTTCCCTAAATTGGgtatgttttc ... ttttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 14

GTTGACCAACTCGTCCTTGAGGAGGTTGTACGAGAAAGGTTCCCTAAATTGGgtatgttttc ... ttttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

GTTGACCAACTCGTCCTTGAGGAGGTTGTACGAGAAAGGTTCCCTAAATTGGgtatgttttc ... ttttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 27

GTTGACCAACTCGTCCTTGAGGAGGTTGTACGAGAAAGGTTCCCTAAATTGGgtatgttttc ... ttttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggttcttgttatggttattacttggcacttacatcaattgcaattttcttcagCCAAACATATGGATTTCTTGGAAGTTCAAGTGGGATGGGTGACTGGACCATGGTTCCTTTCTATTTTCGTCAATATGCTTCCATGGGAAAGTG
                           cacttac  putative branch site (score: 27)
                                             ttttcttc  putative PPT
                ttattactt  TA-rich tract