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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac...

Basic information

species Zea mays
transcript GRMZM2G051270_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgta---tttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgt-ctctgaactaaac-----------------------------------------
||||||||| ||||| |||||||||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||   ||||   |    |||  |||| ||   | |  |    || |     |   || |||  ||||       |  |   |  ||  | | ||    |||                                           
GATGGGTTACAAAAATCCTGTTCTTCTGCTTCATCCATTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtag

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G28980.2 (Glycine max), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataat-tggcttcatgttttctccgcagtagcagctatg-tctctgaactaaac
|||||||||||| || ||||| ||  |||| |||||||||||||| | ||| ||||| |||||||| || |||  |||| ||||||| |||||||||||||| | | ||||   |||    | |  |   | |  |||||   |   |   || |  |||  |||    |   | ||      | |  ||| ||   |    
GATGGGTTATAAGAATCCTGTCCTCTTGCTTCATCCACTGGGAGGCTACACCAAAGCTGATGATGTCCCACTTGATTGGCGAATGAAACAACATGAGAAGgtgtgt-gatgtactaaaccaaata-cttttatagtctcatggttgaagctatgtcactttctgtgcctttttctgttttgattgtaatctttgctttgcta

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G38760.1 (Glycine max), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctc-cgcagtagcagc-tatgtctctgaactaaac-
|||||| ||||| || ||||| ||  |||| |||||||| ||||| | ||| ||||| |||||||| || |||  |||| |||||||||||||||||||||| | | |    | |  ||    | | |  ||| ||   ||  || || |  || ||| | | | ||  | | ||    ||   | ||||||  ||       
GATGGGCTATAAGAATCCTGTCCTCTTGCTTCATCCACTTGGAGGCTACACCAAAGCTGATGATGTCCCACTTGATTGGCGAATGAAGCAACATGAGAAGgtgtgt-gtcaatttctttgcctttttctatttaattgtaa--tcgcattggtttgctacttttcttggcacacacgcacattgtttgtctccaaagatgctt

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G22890.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac
||||||||| ||||||||| ||||| |||| |||||  | || || || ||||| || |||||||| ||| |   |||||| ||||||||||| |||||||||   | |     | ||| |  | |  |  || |     | |      |   |  ||| |  |  |      |   |    ||||  | | ||  |   
GATGGGTTACAAAAACCCTATTCTTTTGCTTCATCCGTTAGGTGGGTTTACAAAGGCTGATGATGTTCCTTTAGATTGGAGGATGAAGCAACACGAGAAGgtaaaaaaagttattgattgttgtgtgtctcttgagtgtgagt-----gtgtgtatcttgaaatgct------aaatgtgtttatgaatgtaaaacag--

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac
||||||||||||||||||| | ||| |||| |||||| ||||||| || |||||||| |||||||| ||||| || ||| ||||||| || || ||||||||||| |        ||| | | |||    || | | |    |  |   || ||   |  | |   |  | | | | |     ||| ||    | ||   
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtattaa-----cggaatcaaagtctttttttgcgtgt----tgtttgctagttcattataggagatg-ctgaattggttttcatgactt--gattag--

upper sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 5'ss of exon 2
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtattta----gatgctataattatactctcccctttcatctcaaattctcaataattgg-------cttcatgttttctccgcagtagcagctatgtctctgaactaaac----------------
|||||| || || |||||||| ||  | || |||||| | ||||| |  ||||| ||||||||||| || ||| ||||||||||||||||||||||||||||   |     ||| |||| ||      |||   ||  |  |||  |   |        |       | | ||||  |  ||  |    ||| | |   |||||   | |                 
GATGGGCTACAAGAACCCTGTCCTCTTACTTCATCCATTAGGAGGCTATACAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAGgttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcag

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|211371619|gb|FL290738.1|FL290738
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32842084|gb|CD981765.1|CD981765
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32840548|gb|CD980229.1|CD980229
EST:     CAAAAGCAGATGATGTGCCTCTTATTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32840519|gb|CD980200.1|CD980200
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32830689|gb|CD970367.1|CD970367
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32836595|gb|CD976273.1|CD976273
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|116828629|gb|EC859788.1|EC859788
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|12046747|gb|BF728886.1|BF728886
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|60350057|gb|DN217030.1|DN217030
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|7304654|gb|AW600593.1|AW600593
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACT
EST: gi|32926464|gb|CF031276.1|CF031276
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32924998|gb|CF029810.1|CF029810
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
EST: gi|32842063|gb|CD981744.1|CD981744
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGTAGAATGAAGCAACATGAGAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagat ... tttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA