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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA

Basic information

species Zea mays
transcript GRMZM2G120373_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g42600.1 (Oryza sativa), 3'ss of exon 3
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcct--aaatgtt-----------------gtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
||||||      |||  ||| |||  |||||    | || | ||||   ||||| |  |  |||||||                 |||||  |   |  || |     |     |      || || ||| || | | ||| ||||||||  |||   | | |||  | ||| ||||||||| |||||||||||| ||||| ||||||||||| || ||||||||||| |||||  ||||||||||||| || || ||||| ||||||||||||||
gtatgtg-----tctcttttctgattaagtatgtcatgaac-ttagtacaatgttgttttcaaatgttccacaattagagctctggtcatgattgcagcttcaatgcttccatcaccctttatgcatattgtttgatccatcctactgaagctaacagcgactttttt-tttctagGTTTAAGAAAGTCCTTGCTGAATGTTTTCCATGATGGATCCTGCCATCCTGGAATGGCCCTAGTAATTGATGACCGACTCAAAGTCTGGGATGAGAAGGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 3
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                                         | ||||   |       ||||| ||   || |  |  ||||      |||  |      |  ||||  | |||  | |  ||||  ||   || |      || |  |||  ||||||||||| || || ||| | ||||| |||||  |||| |  |||||||     |||||||| ||||||||||||||| ||||||| ||||||||||| ||
-----------------------------------------aatagctcga---attttaaattttcaaattcatagcagtttttctgctgcaa------ctgttcatttattttttgtgcttcttgtgtgtttca------atatattata-atagGTTTAAAGAAATCATTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAAGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 3
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattc-tactgaaattaatgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                                                        | | | | ||||   |  | | | |        | |      | |  || |  ||  | ||   | |  || |   ||        |||    || | | |||||| || ||||| ||| | ||||||||||| |||||||| ||  ||||    |||||||| ||||||||||||||| ||||||| |||||||||| |||
--------------------------------------------------------ctttatttttgtaccataccata-tgcctgtgtttttgctgctgctgtttagtttgcttgtcatacttataatatgatggtgtttcaataatataat-acagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTCATGTGATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAGGGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 3
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaatta-atgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                                                       || | | | ||||   |  ||| | |       || |      | |  || || ||  | |  |||| ||  | | ||   ||  |||   | | |  || |||||| || ||||| ||| | ||||||||||| |||||||  ||||||||    |||||||| ||||||||||||||| ||||||| ||||||||||||||
-----------------------------------------------------atgctttattattgtaccatacaata-tgcctgtgcttttgctggttctgtttaatttacttg--tcatacttataatatggtatttcaataatacaa--tacagGTTTGAAGAAGTCATTGTTCAATGTCTTCCAAGATGGTTTATGCCATCCAAAGATGGCATTGGTAATTGATGATCGCTTGAAAGTGTGGGATGAGAAGGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 3
------------------gtatgtaattcatcttgtttttgaacaagta---caaaaagagcattagccta---atgtggcctaaatgttgtcatactcaaaagttgacaaactg---tgaaaaatacaattcaaatttttagtttca----ttctactgaaattaatgccaa---atttcc-tattta-tagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                    ||   |||   ||||||||  ||  || |     | | | | | | |  ||   |   ||   ||||           ||| || |   |   |    |  ||||| ||   ||  ||||  | | ||    |||   |    ||  ||   |    ||||  ||| || |||||||||| || || ||| | ||||| |||||  |||| |  |||||||     |||||||| ||||||||||||||||||||||| ||||||||||| ||
gtaagtggcatttttttaaaattctattatccttgttttcaaatgagaagctttacatgtgtaattgagtagataaagggagcaaataaaaaggatgacaatagcttgtattttaaattttaaaattcataccagtttttctgctgcaactgttcatttattttttgtgtttatgtgtttcaatatataatagGTTTAAAGAAATCGTTGTTTAATGTATTCCAAAATGGCTTATGCCATCTGAAGATGGCATTGGTAATTGATGATCGCCTGAAAGTGTGGGATGAGAAAGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtaattcatcttgtttttgaacaagtacaaaaagagcattagcctaatgtggcctaaatgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcctatt------tatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                                                                                     | ||| |     ||   || |    || || ||||||  |  | ||| |  |  |||  ||   |||       | |||||| ||||||||  || | ||||| || |  |||||  | ||||||||    |||||||| ||||||||||||||  ||||||||||||||||||||||
-----------------------------------------------------------------------------------gtatactttttggtatcttatacctgcttata-tttcatcatggtaaaacttcttacaagcttgtaattaaccaccacagGTTTTAAAAAGTCACTGTTCAATGTGTTTCTCGATGGAACCTGCCATCCAAAGATGGCATTGGTAATTGATGATCGATTGAAAGTTTGGGATGAGAAGGA

upper sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtatgtaattcatcttgtttttgaacaagtacaaaaagagc--attagcctaatgtggcctaa-atgttgtcatactcaaaagttgacaaactgtgaaaaatacaattcaaatttttagtttcattctactgaaattaatgccaaatttcct------attt-atagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                                  | | | ||    |     | ||     || |  |||  ||||     ||     || | ||| | |  |  |||    ||     | | ||  |  |   ||||        |  | |||| | || ||  |  | |  | |||| |      |||| ||||| | || ||||||  || | |||||||| || |||||    |||||||||   ||||| |||||||||||||||||  ||||||| |||||||| || ||
gtaagtttttaaaagaaatggttgatcttagggatgacttatgccatccac-agcagaccaaagacaagctaattaattatatagcttctgatatgat-tttttttcacccattcttgtagt-tgttacttgttattctgtaaaccacgtacattatcctcaatatcctacttattttctttattaaatttgatagGCTCAAGAAAGTCACTGTTCAATGTCTTTCAAGATGGAATCTGCCATCCTAAGATGGCTTTAGTAATTGATGATCGTTTGAAAGTGTGGGATGAAAAAGA

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), 49 (downstream exon)
Score: 130

GAAAGAGACTATGCTTTAGAAATGTGGAGATTGCTTGATCCAGATTCAAGATTGATTAATTCTGTTCAACTCCATGATCGGATGGTGTGTGTAAAATCTGgtatgtaatt ... ctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 100

GAAAGAGACTATGCTTTAGAAATGTGGAGATTGCTTGATCCAGATTCAAGATTGATTAATTCTGTTCAACTCCATGATCGGATGGTGTGTGTAAAATCTGgtatgtaatt ... ctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 71

GAAAGAGACTATGCTTTAGAAATGTGGAGATTGCTTGATCCAGATTCAAGATTGATTAATTCTGTTCAACTCCATGATCGGATGGTGTGTGTAAAATCTGgtatgtaatt ... ctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 127

GAAAGAGACTATGCTTTAGAAATGTGGAGATTGCTTGATCCAGATTCAAGATTGATTAATTCTGTTCAACTCCATGATCGGATGGTGTGTGTAAAATCTGgtatgtaatt ... ctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaaatttttagtttcattctactgaaattaatgccaaatttcctatttatagGTTTAAAAAAGTCCTTGCTAAATGTCTTCCATGATGGTTCTTGCCATCCTGGTATGGCATTAGTAATTGATGATCGCCTGAAAGTTTGGGATGAGAAGGA
                            aattaat  putative branch site (score: 127)
                                         tttcctattt  putative PPT
     aatttttagtttcatt  TA-rich tract