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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaaaaaacttagtttcttgttttctccaattggtaagtgtttacttgaatatatcaattcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA

Basic information

species Zea mays
transcript GRMZM2G443953_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------gtattaaaaaa-acttagtttcttgttttctccaattggtaagtgtttacttg-----aatatatca------attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
                                                                     || | |||     | |   || |    || ||  ||   ||| | ||| ||       || || |        ||||| |||| || |||||||| ||||| ||||||||||| ||| | ||  |||| || |||| |||||| ||||| ||||| | |||||| ||||| || ||| | || 
gtaagttttttctggatagaaattttgtaagtaatttcttaggccgttgaataatctgagtgggaaactgtgtcaaattgtgcctgaattatgaaattttcttatctttaactcttttctcataatcaaaattttcgggtgcattcaaacagGGTTGTGATTGGCTATGATGAAGGAACAATTATGGTCAAACTTGGTCGAGAAGTACCTGTGGCTAGCATGGACAACAGTGGGAAAATTATTTGGTCTAAG

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 9
----------------------gtattaaaaaaacttagtttcttgttttctccaattggtaa---gtgtttact-----tgaatatatcaattcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
                      || ||  |   |      ||      || |  || || | |   | |   |        |||| | |    |  ||||| || |||||||||||||| |||||||| || ||| ||||  |||| || |||   ||||| ||||| ||||| || || || |||||||||||||| || 
agggcgtttagagtggctaggagttttttagggatcagtgttagcaccttattaaactgatcatacgggaccatcaacaacgaatgtgtttgctt-tacagGGTTGTGATTGGATATGATGAAGGAACCATCATGGTTAAACTTGGACGAGAAATTCCTGTCGCTAGCATGGACAGTAGCGGAAAAATCATATGGGCTAAG

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 10
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------------------------------------------------gtattaaaaaaacttagtttcttgtttt-ctccaattggtaagtgtttacttgaatatatcaat-tcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
                                                                                                                                || |   |  |  || | |  || | |    |||  |   | | ||   || | | | | | |  | ||| || |  |||||||| || |||||||| || |||||||| || ||    || ||||| |||||||| |||||| | |||||||||||||||||||| |||
gcgagttctctaccaaaacgtttgaactcaacgtattgtatcttttaggcggtttaacaagttattcttaagacatatacaaggatatcatttaattttttcacctaaaacatcctgttacacactccttcattgatgtgtgtgtgtaattctgcgtttattcatttatatgtatgggattgtcttattattgtgcagGGTGGCAATTGGATACGATGAAGGAACTATCATGATTAAAATGGGAAAGGAGGCACCAGTTGCTAGCATGGATGGTAGTGGTAAAATCATATGGGCAAAA

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: 49 (upstream exon), 45 (downstream exon)
Score: 134

GCTTGAGAATACACTTAACTATGGCCTTGAACGAGTTTGGGCATTAGGTTACATGAAGGGCTCACGAAGgtattaaaaa ... attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 80

GCTTGAGAATACACTTAACTATGGCCTTGAACGAGTTTGGGCATTAGGTTACATGAAGGGCTCACGAAGgtattaaaaa ... attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 36

GCTTGAGAATACACTTAACTATGGCCTTGAACGAGTTTGGGCATTAGGTTACATGAAGGGCTCACGAAGgtattaaaaa ... attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 75

GCTTGAGAATACACTTAACTATGGCCTTGAACGAGTTTGGGCATTAGGTTACATGAAGGGCTCACGAAGgtattaaaaa ... attcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttgttttctccaattggtaagtgtttacttgaatatatcaattcatacagAGTCGTGATTGGATATGACGAAGGAACAATAATGATTAAGATTGGGCGTGAAGCACCTGTTGCTAGTATGGATAGCAGTGGTAAAATCATATGGGCCAAA
                                    aatatatcaattcata  TA-rich tract