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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttcctgagtcccaacaagcctattattcaacttaagaatttcagctggttgcccgtgctttgctatgatttttatatatcatataaat...

Basic information

species Zea mays
transcript GRMZM2G029530_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 5'ss of exon 6
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttcctgagtcc-caacaa-gcctattattcaacttaagaatttcagctggttgcccgtgctttgctatgatttttatat-atcatataaat
|||||||||||| ||||| ||||||||| |||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||| ||  | | |   | ||||    ||  ||   |  |       ||||||  | |     |      ||   | || |||  ||||       
TGATGTATATAGTTTTGGAGTTGTTCTTCTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCACACAATGCCTAGGGGTCAGCAGAGTCTGGTTACATGGgtaagcattttatttgtaaatttactacaatatttaacatgagagctgtttgcctcagctattggtaaaaggagaattactttgttgataagatcactct---

upper sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G38980.1 (Glycine max), 5'ss of exon 7
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttcctgagtcccaacaagcctattattcaactt---aagaatttca-gctggttgcccgtgctttgctatgatttttatatatcatataaat------
|||||| ||||| ||||| ||||||||| | |||||||| |||||||| ||||| || || ||||| ||||||||||| ||||||||||| || |||||||| ||  | |        | ||  | |    |  |  | |  |||   ||  |||| |  ||||||| | |  | | | |||  | || | || | ||||   |      
TGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgtctgcttaaactcatacctcatccgtgctgctgcttttcaatcatttaacactggttgtcggc-cataggtattttgttgacat-tgatatttttttgtag

upper sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G44210.1 (Glycine max), 5'ss of exon 7
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgtt----cctgagtcccaacaagcctattattcaacttaagaatttcagctggttgcccgtgctttgctat-gatttttatatatcatataaat
|||||| ||||| ||||| || |||||| | |||||||| || || || ||||| || || ||||| ||||||||||| ||||||||||| || |||||||| ||  |  || |    |      | || |    || || |||||      |      | ||   |||   | | |  | | ||| || |||| |  | ||   
TGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACCATGCCTAGAGGACAGCAGAGTCTTGTCACATGGgtcagtgtgctgcttaaactcatacctcatcgctgctgtttttcaatcatttaccactggttgtcagccatagatattttgttgatattgatattttttgtag--

upper sequence: GRMZM2G029530_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 5'ss of exon 6
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttc---------ctgagtcccaacaagcctattattcaacttaagaatttcag--ctggttgcccg----tgctttgctatgatttttatatatcatataaat-------------------
|||||| ||||| ||||| |||||||| |||||||||||||| || || ||||| || |||||||| |||||| | || || || |||||||| || |||||  |  |||| |||         ||   | |  | |||||| || |||| |    |  |||||    |   | | |     |||||| || |||| | ||| ||| || ||||                    
TGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACCATGCCTCGTGGACAACAAAGTCTGGTCACCTGGgtgggttttttcttctttttctgcctatttgcttaaaagccttttgttcacccagtgcctttcaagtttctctactccaaattgcttttctttgatatatatctataatctaaagtgaacatttctcatcttag

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|76935777|gb|DV174468.1|DV174468
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|18649452|gb|BM498271.1|BM498271
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|89764339|gb|DY691183.1|DY691183
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|67043118|gb|CO469373.1|CO469373
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|18383742|gb|BM416942.1|BM416942
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAANCAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|67032611|gb|CO461360.1|CO461360
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|18450374|gb|BM428652.1|BM428652
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|4827765|gb|AI668457.1|AI668457
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
EST: gi|78026567|gb|DV494954.1|DV494954
EST:     AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGGGTCTGGTTACATGG                         GCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA
genomic: AACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGA

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: 66

TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 50

TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 66

TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 89

TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattt ... atttattcagGCAACACCTAGATTGACTGAGGACACAGTTAAACAATGTGTTGATCCAAGATTGAAGGGAGAATATCCTCCAAAGGGAGTTGCCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACAATGCCTAGAGGTCAGCAGAGTCTGGTTACATGGgtaagcattttgttcctgagtcccaacaagcctattattcaacttaagaatttcagctggttgcccgtgctttgctatgatttttatatatcatataaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA