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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattctcatacatatccggcaaacattttatctgggcttgataactatttttcctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA

Basic information

species Zea mays
transcript GRMZM2G104254_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104254_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------gtagattctcatacatatccggcaaacattttatctgggc---ttgataactatttttcctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA
                                                       |||  |   ||  ||    ||     | ||    ||||    ||| | ||   |   | |  || ||||| ||| |  | || || || || ||| | || ||||||||| | || || ||| | ||||||||||| ||||| |||||||||||| | |||||||| |
gtaagcatttgcttttgaagatttgtacaagttcattctcttccttgagttgctttagtgttcaatgaat---tggtcggtacttagcatgggtgtattgttgacatctacccttcactgcagAAAGAGGGACAATTGACACTTCGTGACCTGAAGCGGTGTAAATTATCTGGGAATTTTTTCAATATTCTCTTCAACCTGAACAAGTTCGTAGCATTTGAGA
















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: 185

TTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAGGAACCTGTGGTTTTTGGGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

TTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAGGAACCTGTGGTTTTTGGGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

TTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAGGAACCTGTGGTTTTTGGGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAGGAACCTGTGGTTTTTGGGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctc ... ctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatatccggcaaacattttatctgggcttgataactatttttcctttctacagAATGAGAGCTATTTTACTCTACGGGACTTAAAACGGTGTAAACTCTCAGGAAATATATTCAATATTCTTTTCAATCTGAACAAGTTCATGGCATTTGAAA
                              tgataac  putative branch site (score: 91)
                                    ctatttttcctttcta  CT-rich tract
                             ttgataactattttt  TA-rich tract