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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacacaaatatgtgtttagatcccaattatgcatgaggtgaaagagataaatgttcaatgttctgactggatatcaatatgcttgtttgttttactcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG

Basic information

species Zea mays
transcript GRMZM2G171604_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 4
gtaaacacaa----atatgtgtttagatccc-aattatgc-------------atgaggtgaaagagataaatgt-tcaatgttctgact--ggatatcaatatgcttgtttgttttactcatc-cagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG
|||||  | |    || |||  ||||||||| |||  |||             ||||| | | ||||| | || | |  || ||   |||  |||  | | |||  ||   |  |||||||||  ||||||||||||||||| ||||| || |||||||| ||||| |||||||| |||||||| ||||||||||||||||||||||||||||||
gtaaatcctacattatttgtacttagatccctaatagtgcatgtaatgtgactatgagatcacagagacatatatatggatattgcaactatggaagttattatattt---tactttactcattgcagGGTGTTCTACTCTATGGTCCACCAGGAACTGGTAAGACACTATTGGCGAGGGCTATTGCCAGTAACATCGATGCCAACTTTTTGAAG

upper sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ13668 (Selaginella moellendorffii), 3'ss of exon 4
gtaaacacaaatatgtgtttagatcccaattatgcatgaggtgaaagagataaatgttcaatgttctgactggatatcaatatgcttgtttgttttactcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG
                                               |  |    | | ||  |  |  || | |||||||||  |    |||| ||        ||| ||  | || ||||| ||||| || || || ||||||||| |||| || ||||| || |||||||||||||| |||||| |||| 
--------------------------------------------gtaaattgcgagcttaacttgtt--cttgttatcaatattttcaactgttgta--------gGGAGTGTTGCTATACGGGCCTCCAGGGACAGGAAAGACCCTACTGGCGAGAGCTATTGCAAGTAACATCGATGCTAACTTTCTGAAA

upper sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28962 (Selaginella moellendorffii), 3'ss of exon 4
gtaaacacaaatatgtgtttagatcccaattatgcatgaggtgaaagagataaatgttcaatgttctgactggatatcaatatgcttgtttgttttactcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG
                                               |  |    | | ||  |  |  || | |||||||||  |    |||| ||        ||| || || || ||||| ||||| || || || ||||||||| |||| || ||||| || |||||||||||||| ||||||||||| 
--------------------------------------------gtaaattgcgagcttaacttgtt--cttgttatcaatattttcaactgttgta--------gGGAGTGCTGCTATACGGGCCTCCAGGGACAGGAAAGACCCTACTGGCGAGAGCTATTGCAAGTAACATCGATGCTAACTTTTTGAAA

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|31356451|gb|CD440808.1|CD440808
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149076338|gb|EE164954.2|EE164954
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAGGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|21760157|gb|BQ635698.1|BQ635698
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148999624|gb|EE036609.2|EE036609
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149111231|gb|EE294729.2|EE294729
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|87157334|gb|DY402123.1|DY402123
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|211475166|gb|FL103099.1|FL103099
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACT-GGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|26559696|gb|CA831931.1|CA831931
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTG
EST: gi|148936301|gb|EC880384.2|EC880384
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|21843335|gb|BQ703916.1|BQ703916
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGA
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGA
EST: gi|93284400|gb|EB676664.1|EB676664
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149080389|gb|EE169410.2|EE169410
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148959843|gb|EE153075.2|EE153075
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148953590|gb|EC898944.2|EC898944
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|22935727|gb|BU572002.1|BU572002
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148967099|gb|EE018270.2|EE018270
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148942358|gb|EC887376.2|EC887376
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAGGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|5325115|gb|AI783306.1|AI783306
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|20803091|gb|BQ294141.1|BQ294141
EST:     ACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTTAAGCCTCCTAAG                         GGTGTTCTACTCTACG
genomic: ACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATT-AAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACG
EST: gi|211472646|gb|FL103083.1|FL103083
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|31358883|gb|CD443240.1|CD443240
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATT
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATT
EST: gi|148931017|gb|EC873580.2|EC873580
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|67033051|gb|CO461800.1|CO461800
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148979144|gb|EE026532.2|EE026532
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|67024916|gb|CO453665.1|CO453665
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|148964792|gb|EC906040.2|EC906040
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149112655|gb|EE191390.2|EE191390
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149100597|gb|EE186683.2|EE186683
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|149009942|gb|EE041784.2|EE041784
EST:     CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAG                         GGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
genomic: CACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGG
EST: gi|511349|gb|T23327.1|T23327
EST:     CTTATGAACCCCTGAACTCTTTCTTCGGGTGGGAATAAAGCCTCCTAAAG                         GGTGT-CTACTC
genomic: CTTATGAACCC-TGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAA-Ggtaaacacaa ... actcatccagGGTGTTCTACTC

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), 48 (downstream exon)
Score: 280

AGGCGGTTTGTCTGATCAGATTAGGGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

AGGCGGTTTGTCTGATCAGATTAGGGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

AGGCGGTTTGTCTGATCAGATTAGGGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

AGGCGGTTTGTCTGATCAGATTAGGGAGCTCAGGGAGTCCATTGAGTTACCACTTATGAACCCTGAACTCTTTCTTCGGGTGGGAATTAAGCCTCCTAAGgtaaacacaa ... actcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgttcaatgttctgactggatatcaatatgcttgtttgttttactcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG
            ttctgac  putative branch site (score: 213)
                                         ttttactc  putative PPT
                      atatcaatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacacaaatatgtgtttagatcccaattatgcatgaggtgaaagagataaatgttcaatgttctgactggatatcaatatgcttgtttgttttactcatccagGGTGTTCTACTCTACGGTCCTCCGGGAACTGGGAAGACCCTATTGGCAAGGGCTATCGCCAGTAACATCGATGCCAACTTTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG