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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgccttctcaaaatttagcgaagccacgcgaatccatacttgattttgatgtccccggttggagcaccgggtgacaattcagtagtacagtgg...

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 5'ss of exon 2
CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgccttctc-aaaatttagcgaagccacgcgaatcc-atacttgattttgat--gtccccggttggagcaccgggtgacaattcagtagtacagtgg
|||||||||||||||| | |||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||| ||| |||||| || | | ||| |||||||   |  | || | ||||   || ||| |      |  ||   |  ||     | | | | |   | | |   | |||   
CAACAAGGACAAGGCCATGTTCACCATTGTCGTCTCCGGCACGGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAACAAGCTTGTCAACGTCTTGAATgtgagcccccttgctccaaaatttgttggggtcatgtgaatttgatgcttaaaccaatttagtttgccatttatagatctgataagcttccggccct-cag---

upper sequence: GRMZM2G407044_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA05G30130.1 (Glycine max), 5'ss of exon 2
CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgccttctcaaaatttagcgaagccacgcgaatccatacttgattttgatgtccccggttggag-caccgggtgacaat--tcagtagtacagtgg---------------------------------------------
|||  |||||| ||| ||||||||||| ||||| || |||||||| | ||||||   ||||||||| ||||||||  | || || ||||| ||| | |  ||    |  | || ||   |  || | |  ||  |  | |      || ||| || |||    |   |  | ||   || || | |  |   ||||  | |                                               
CAATGAGGACAGGGCTCTCTTCACCATCGTCGTGTCAGGGACCGATAAGGTGCTGCGCCAAGTCATGGAGCAGCTTCAGAAACTCGTCAATGTCTTAAAGgttcaccgtctttttcgtgacataccaattccgtgtaactggcgtttttattgtg-tgtttttgtgagatgtcatttggagaaagtgtttgatagtgaaattagtgagagattgaatctgaaggaaacgtgttgctaatgctggctag
















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|211258838|gb|FL034314.1|FL034314
EST:     GCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTNGAGT                         GTGGAAGATCTATCTAAAGAACCTCA
genomic: GCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCT-GAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCA
EST: gi|148959834|gb|EE153063.2|EE153063
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|211258845|gb|FL034321.1|FL034321
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTA
EST: gi|33098451|gb|CF058411.1|CF058411
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|149075260|gb|EE163764.2|EE163764
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|211261273|gb|FL034327.1|FL034327
EST:     GCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTNGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTAT
genomic: GCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCT-GAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTAT
EST: gi|78122764|gb|DV541148.1|DV541148
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCGGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|148949305|gb|EC894756.2|EC894756
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|71435773|gb|DR816823.1|DR816823
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
EST: gi|149087824|gb|EE177122.2|EE177122
EST:     TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGT                         GTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA
genomic: TGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATA

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: 165

CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgc ... tcgattacagGTGGAAGATCTATCTAAAGAACCTCAGGTTGAAAGAGAGCTGATGCTTATAAAACTAAATGTTGAACCTGATCAGCGTCCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACAAGGACAAGGCCCTCTTCACCATTGTCGTCTCCGGGACCGACAGGGTGCTCAACCAAGTCATCGAGCAGCTCAATAAGCTTGTCAACGTCCTGAGTgtgagtccgccttctcaaaatttagcgaagccacgcgaatccatacttgattttgatgtccccggttggagcaccgggtgacaattcagtagtacagtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA