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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt...

Basic information

species Zea mays
transcript GRMZM2G064695_T04
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatat-tagtggtgcatgcttgatgcttctgtta-gtcttcc--cgtaggaggcccttg-agtaaacccagatctattattcttgcctgtctt
||||||||||| || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||| |  |  |   ||  | |  |   |  | |     ||||  | ||| |||  |   |||  |  | | |    ||   ||| |  | ||   |        
GTTGACCTGAAGGTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag--------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g40830.2 (Oryza sativa), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatat-tagtggtgcatgcttgatgcttctgtta-gtcttcc--cgtaggaggcccttg-agtaaacccagatctattattcttgcctgtctt
            || |||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||||| |  |  |   ||  | |  |   |  | |     ||||  | ||| |||  |   |||  |  | | |    ||   ||| |  | ||   |        
------------GTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAGgtaaaaattacttgcatgcattctttttttgtaggaatatctgccaagtcgtccttcactggaaactttcgtacctgactgtgatgtcctgttgcag--------

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt
||||  |||||||| || ||||| |||||  |||||||||||||||| || |||||||| || ||  | |||||||    ||||    ||| |  |  |  |||   |     |      |     ||| | |  ||| |         |||     ||  ||         
GTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAGgtaaa---tgttagatttattaatataatcttatagaaaacgaagcattaatgttagcaagtgcttaatatgtttttgatactcaatgattcaacag---

upper sequence: GRMZM2G064695_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 11
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttc-tgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt-----
|||   || ||||| || || ||||||||| | |||||||||||||| ||||||||||| || ||||| |||||||  ||      | |   |||       || ||      ||||         | |  |    |   |  | |    ||  | ||  ||     ||   |     
GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAGgtaaatgcaaaacctttggatggaattcaatttatttcgagtgtttccaaaaaggaaaaaaaatcagaaacataatacgagttgttgatcacaaatgatattgcag

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|113853280|gb|DW973854.1|DW973854
EST:     TTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAAAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|113791641|gb|DW913466.1|DW913466
EST:     GGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: GGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|18162086|gb|BM331925.1|BM331925
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|166652168|gb|EG083409.1|EG083409
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAAAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATG
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATG
EST: gi|113831703|gb|DW948357.1|DW948357
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATC
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATC
EST: gi|211240437|gb|FL261944.1|FL261944
EST:     TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAR
genomic: TTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
EST: gi|166626099|gb|EG158853.1|EG158853
EST:     GTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG                         GAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG
genomic: GTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAG

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: 48 (upstream exon), 49 (downstream exon)
Score: 633

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAGAAAGCTGTAAAAGCATCCGTCAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1037

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAGAAAGCTGTAAAAGCATCCGTCAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1145

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAGAAAGCTGTAAAAGCATCCGTCAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 891

GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctg ... tatcttgcagGAAAGTGGAATGACTTTGATCACTGCAGAAGATCTTGATGATGCGGCAGAGAAAGCTGTAAAAGCATCCGTCAAATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAGgtaagagctgttgatattagtggtgcatgcttgatgcttctgttagtcttcccgtaggaggcccttgagtaaacccagatctattattcttgcctgtctt

- - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT