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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatgtccatatgatcctactttttttatccttttatactagaatagtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt...

Basic information

species Zea mays
transcript GRMZM2G177914_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 5'ss of exon 6
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatgtccatatgatcctactttttttatccttttatactagaat-agtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt
| ||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||   |   | |  ||| |   |   ||||  |     ||| ||  | | ||  ||    |  || ||  |        |   |  | ||   | | | |
TTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTGACATCGTATTTAACTTCAACAAGgtaaagtg-attctcatgttttgatccttttactttgaatatgctccattgaggctgggcttgaagaatataaaagggtcaagttcataaagcatgcttat

upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 5'ss of exon 5
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccat-atgtccatatgatcctactttttttatccttttatactagaatagtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt
| ||||||||||||||||||||||||||||||||||| || |||||| |||| |||||||||||||||||||||     || | ||| |  |  | |||||  | |   | |   | |     |  || || |  || ||  |        |      | ||   | | |  
TTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAGgtaaagcgattttcatgttttgatccttttactttgaatatgctccattgaggcttggct-tgaagaatataaaagggtcaagtaaataaagcatgcttgg

upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G06350.2 (Glycine max), 5'ss of exon 6
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgt-----accatatgtcca-----tatga-tcctactttttttatccttttatactagaatagtgtgcctatcgaggatgca-tggtttctatcctgctgaaaattccattt
|| |||| ||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||||      |  | || ||      ||||| || ||  ||| ||     || |  | |  ||| ||| ||| |  || | | | ||  ||  |  |||               
TGCTTGTGGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAGgttgtatgctttgtgccccccgattatgaatcttatatttatttcaagttgactccattataatgtacctctgtagcaagaaatgaatttgaaactgtgt------------

upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G25400.1 (Glycine max), 5'ss of exon 6
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccata---tgtccatatgatcctactttttttatccttttatactagaatagtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt
||||||||||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||||   ||    ||| |   ||||  |   | || |||   |||  | |  | |    |   ||  | |  |   | |     |      |  ||| |  ||| 
TGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAGgttgtatgctttgtgcccctgattatgaatcttatatttatttcaaattaactctatta--taatgtgcctctgtagcaagaaatgaattagaaactgtatt-

upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 5'ss of exon 5
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatgtccata--tgatcctactttttttatccttttatactagaata-gtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt
|  | || |||||||||||||  |||||||| |||||||||||||||||||| || || || |  | ||||||   || |   | |   | ||  | |||  | |  | ||| || || | | | | || | |    || | |      |  |  |   |   |  ||| ||  
TTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAGgtgatattttctcctccctcattttgcttggtgtcacttttaatgcttggaaatgggtactttattagcaggt-caaatattgactaacattattttctat--

upper sequence: GRMZM2G177914_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S128_112V6.1 (Physcomitrella patens), 5'ss of exon 5
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatgtccatatgatcctactttttttatccttttatactagaatagtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt--
||||||| || ||||||||| |||| ||||||||||| || |||||||| || || |  ||||||  |||||||  |  | ||    | |        |||| ||| |   | || |  | |   ||||  |  |     |   |       | || ||||   |  ||    
TGTTTGTAGAGACATTGGACCGATGTTTCAAGAATGTCTGTGAGCTTGATATAGTTTACAACTTCGGCAAGgtaagaactttctcagttagaacttggttttgatcatcacaaacaatgagaa-atgccacttcaattcac-cagcaatagacttgatgaagtatggatagcg

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|71436744|gb|DR817794.1|DR817794
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCAAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|71758093|gb|DR956030.1|DR956030
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|84980466|gb|DW530815.1|DW530815
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACGATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|78110300|gb|DV528715.1|DV528715
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|211467090|gb|FK972969.1|FK972969
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTG
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTG
EST: gi|211467088|gb|FK972967.1|FK972967
EST:     TGCTTTCA-GAATGTATGCGAGCTTGACATCGTATTTAACTTTCAACA-G                         CTGCACAC-ATTTTGGATGAGATGATATC
genomic: TGCTT-CAAGAATGTATGCGAGCTTGACATCGTATTTAACTT-CAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATC
EST: gi|71771237|gb|DR969174.1|DR969174
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|19769487|gb|BQ034208.1|BQ034208
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAGCTTCGACGAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|211469615|gb|FK972982.1|FK972982
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCNNNNNNNNACAGGGTGATCGAA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGG--ACAGG-TGATCGAA
EST: gi|18162805|gb|BM332644.1|BM332644
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|9742647|gb|BE518795.1|BE518795
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|37379099|gb|CF626280.1|CF626280
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACTCCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|78110301|gb|DV528716.1|DV528716
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|148948825|gb|EC894231.2|EC894231
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|149107282|gb|EE189165.2|EE189165
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|211467091|gb|FK972970.1|FK972970
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
EST: gi|149107281|gb|EE189164.2|EE189164
EST:     GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG                         CTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA
genomic: GATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatg ... tctgatgcagCTGCACACCATTTTGGATGAGATGATATCGGGGGGACAGGTGATCGAAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGgtaccatatgtccatatgatcctactttttttatccttttatactagaatagtgtgcctatcgaggatgcatggtttctatcctgctgaaaattccattt

- - - - - - - - - - - - - - - - - - - -  GAGCTT