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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagggatctctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 10
gttag-ggatctctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
||| | ||||||||||| ||  | |   |||  |        ||  | |||  | ||   |||||  || |||  | |   || |||||||||||||||||||||||||||||||||||||||| ||||||||| | || |||||||| |||||  |||| ||||| |||
gttggtggatctctaat-tccatagcactttagtt-------ctacactgatgtaaccttctcacaaaatttt--tccaactgcagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCT

upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G01850.1 (Glycine max), 3'ss of exon 10
------------gttagggatctctaatctctgtggtgtttttt-tcatttcagctgtaatgagttgacaagctcacctaagtttgatt-----ctcgtgt--agCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
             |         |||    ||   || || | | | || | | |  |||    |  | |    ||   |    ||| |     || |  |  || |||||   ||| | ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || || |||||||||
gttagcagttctttcctctgctgctacctgctaaagtattatatgtaatataatccataaatgataaatacttccattcagacctgactgaaaactggcttccagGTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCT

upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagggatctctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaa-gtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
||| |  |    ||||| | |  |  | |||      |  ||| |  | |  ||| ||  | |  ||   | | | |||     || ||||    ||||| |||||||||||||| || || ||||| ||||| || |||||||||||||||||||| || |||||||| 
gtttgttaaa--taatcgcaggtgcctctttggtgcgtgtgct-tgttcaaatga-aatttaatgtagcatataactctt---cagATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCA

upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
--gttag-ggatct---ctaatctctgtggtgtttttttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgt---------agCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
  |  ||  ||||    ||  | | | | ||| ||     | |   | | |   |  ||  |     || |   ||  |    | ||||         || ||||    ||||||||||| || ||||| || ||||| || |||||||||||||||||||| || || ||||| |||| ||||
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT

upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------------------------------------------gttaggg-atctctaatctc---tgtggtgtttttttcatt--tcagctgtaatga-gttgacaagc-tcacctaagtttgattctcg---tgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
                                                                                    ||   || ||   || |  |    || ||| ||| ||   |  |  | | | | || | | ||  || |    || |   |||    |   || || ||||    || ||||||||||||||||| |||||  | ||||||||||| ||||||||||| ||||| ||||| ||||  |||
gtatgttttttgtgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcagGTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|213179091|gb|FM180755.1|FM180755
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|60399462|gb|DN232274.1|DN232274
EST:     CTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: CTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|31664051|gb|CD573231.1|CD573231
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|5607686|gb|AI901353.1|AI901353
EST:     ATT-TT-TG-ATTC-AGTTCCCTCA-AT-AAAG-CCATCCATGGC-CAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|116824778|gb|EC868424.1|EC868424
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|60354737|gb|DN221710.1|DN221710
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|60338924|gb|DN205897.1|DN205897
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|21626337|gb|BQ621258.1|BQ621258
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGCCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
EST: gi|78025807|gb|DV494194.1|DV494194
EST:     ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG                         CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA
genomic: ATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTA

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: 651

ATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

ATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

ATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 139

ATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAGgttagggatc ... tctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatttcagctgtaatgagttgacaagctcacctaagtttgattctcgtgtagCTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT
                                            ttctcgt  CT-rich tract
                                   taagttt  TA-rich tract