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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccactctctattcgacagttcattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG

Basic information

species Zea mays
transcript GRMZM2G104920_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
gtatccact-ctctattcgacagttcattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgct-agAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
||||    | |||| ||| |||||||||| ||||     ||| || |  |   ||||  |    ||| | | | ||||||    | |  | ||||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||| |||||  | || ||||||||||||||||||||||||||||||
gtatttcttgctctgttccacagttcattttgca-cacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 8
----------------------------------gtatccactctctattcgac--agttcatt-------ctgcaatggc-tgtattgtaattcaaactgaggcatatggttt--------ctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                  |||||  |||| |      |  | ||||||        |  |||| | |||  | |  || ||  |    || ||  |||        || |   || | |  |   ||||| | |||||||||||||||||||| ||| | ||||||||||||||||||||  | |||||| | || ||||| |||||||| || ||||| || |||
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagctctttgggtatcttaattcattaatatttttttaatgtcatgtgct-tgcttaaattttctacagattatttactcatggctatcatttttccttttgcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
----------------------------------gtatccactctcta------ttcgacagttcattctgcaatggctgtattgtaattc----aaactgaggcatatggtttctgtgta--------ttgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                  |||||   ||| |       |||     || ||  ||   ||  |||  |||  ||     |   |    || ||  |||  |  |         ||   |  ||  ||||| | |||||||||||||||||||| ||| | ||||||||||| || |||||  | |||||  | || ||||| |||||||| || ||||| || |||
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgcttaagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 8
----gta-tccactctc--tattcgacagttcattc-tgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
    ||| |  || |    |||   |||   ||    |   ||     | |  | | |    | | |   |    ||| | ||||     |   |  ||||| | ||||| ||||||||||| || ||  | || ||||||||||| ||||| || |||||  | |||||||| |||||||| ||||| || ||||||
gtgagtactttacccaaagtatctaacatcgcacctataagatattcatctcatgaattctgcagcgtatttgaatttttatgta---aactgaggcagAGTCTTATGGAGTATGAAGAGCACGAAAAACGTGCCTGGAGTGTTGACTTTTCACGAACAGAACCATCAATGCTTGTATCTGGTAGTGACGACTGCAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtatccactctctattcgacagttcattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
             |   | |||    ||| ||  | | | |  | | |   |  | || |  | |   |   ||||   | ||    | |||    |   |||||||||||||||||||||||||||| ||  | |||||||||||||||||||| ||||||||  | |||| ||| |||||||| ||||||||||| |||
ggtcctttgaatgaaaaattctgggctcgcca-ctgactatagatttgtccttgtata-tatatatatatatatatatatgctaataaatgttttttatcagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------gtatccactctctattcgacagt-tcattctgcaatggctgtattgtaat-tcaaactgag---gcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                     | ||   | ||| |   | | |   |||||| |  |  | || |||  ||  | |||    |  | || |  ||  |  |  |    | |||||||||||||||||| || |||||||| ||| |||||||||||||||||||||| ||||| ||  |||||||||| ||||| || |||||||| ||||||
gtagaaattgtatctcttctcttctgttaatctcaattacatcatatatgcacaaatgttgatctgcattcacaattttctaacctcccaatgatttcgagtttgttcactaagattctttttcttctagAGTGTGATGGAATACGAGGAGCATGAAAAGCGAGCATGGAGTGTTGATTTTTCACGCACTGAACCTTCAATGCTCGTATCCGGCAGTGATGACTGCAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------------gtatccactctctattcgacagtt---cattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgt-attgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                                                               ||| || ||    ||  | | ||   |    |||   || ||||  ||   || || |     | ||| | |   ||  ||  |    | | ||||||| ||||| ||||| ||||| |||||| | || ||||||||||| ||||| || || ||  |||||||||| || ||||| ||||||||| |||||
gtaggcttgaaaatttggccacttaacataggttcgttgatgatgtccttaattgtggttccagaatgagcgacatatagctttacaatgtgtcatattcattcggatttttaaattttgacgcattgcttcggatgtacggtttgtctaaatatttgacatgttctgcttgccatcatatattaccagAGTGTCATGGAGTATGAGGAGCACGAGAAGCGTGCCTGGAGTGTTGACTTTTCCCGGACGGATCCTTCAATGCTGGTCTCTGGAAGTGATGATGGCAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------gtatccactctctattcgacagttcattctgcaatggctgtattgtaattcaaactga--ggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                 |      | | | |  |   ||   ||      |  ||      ||||      |||  |||    | |||   |  |   |    |   ||||  | ||||||||||| |||||||| ||||| || |||||||| |||||||| || || ||  |  | |||||||| || || ||||||||| |||||
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S180_148V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------gtatccactctctattcgacagttcattctgcaatggctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
           |      |  ||     || |  | | |  |  |     || |  |  |   |  |  |  || |    |  ||   ||||  | ||| ||||||||||||||||||| || ||||| ||| | || |||||  | ||||||||||| |||||  | |||||||| || ||||| ||||| ||| | |||
atacaagatgagggggagcaatcctagagaaaaattagtacgtgagtaaggtttacttgtgttacttatgttatctt-cctaagtaatttgtttcgtgc-agAGTGTGATGGAATATGAGGAACATGAAAAGCGTGCTTGGAGCATCGATTTTTCTCGTACAGATCCATCAATGCTGGTTTCTGGAAGTGACGATGGAAAG

upper sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------gtatccactctctattcgacagttcattctgca-----atggctgtattgtaattcaaactgaggcatatggtttctgtgta---ttgtgcc-atgct--agAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
                                                                          | || | |   |  |  |   |   | ||        || |||   |||  |||    | |  ||      ||||  ||    ||||    |||||  ||||  | | ||| |||||||||||||| ||||| ||||||||||| |||||||| || || ||  |  | ||| |||| || || || |||||| |||||
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 24

TAAACTTAGCTGCCTAAGCTGGAACAAGTACTCAAAAAATATTATTGCAAGCAGTGACTATGAGGGTATAGTAACTGTGTGGGATGTTCAGACCCGTCAGgtatccactc ... gccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG


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

TAAACTTAGCTGCCTAAGCTGGAACAAGTACTCAAAAAATATTATTGCAAGCAGTGACTATGAGGGTATAGTAACTGTGTGGGATGTTCAGACCCGTCAGgtatccactc ... gccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 34

TAAACTTAGCTGCCTAAGCTGGAACAAGTACTCAAAAAATATTATTGCAAGCAGTGACTATGAGGGTATAGTAACTGTGTGGGATGTTCAGACCCGTCAGgtatccactc ... gccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

TAAACTTAGCTGCCTAAGCTGGAACAAGTACTCAAAAAATATTATTGCAAGCAGTGACTATGAGGGTATAGTAACTGTGTGGGATGTTCAGACCCGTCAGgtatccactc ... gccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtattgtaattcaaactgaggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
     attgtaatt  TA-rich tract