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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtacttttaacttgatttgtttccagaaggttacacatttattggtggtgattttgaatgggttaaatcaatttctgaatgtacctgctagtttgt...

Basic information

species Zea mays
transcript GRMZM2G062416_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062416_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 5'ss of exon 10
GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgt-acttttaacttgatttgtttccagaaggttacacatttattggtggtgattttgaatgggttaaatcaatttctgaatgtacctgctagtttgt----------
|||||||| || ||||||||||| |||||||||||||| || |||||||| || |||||| || |||||| |  | | || ||| | ||||| |     |||||   |||||  ||| |    | | | | ||  ||||  | |||||||||||              
GATTTTGGTGATAGCATACCTGGCCATGGTGGATTTACTGACAGGATGGATTGTCAAgtaagttactttttaagttaatttttttctgaaggctg----tttat-aatggtgtctttca----gatgagtaaacctctg--tatacctgctagtgctctcgtagtata

upper sequence: GRMZM2G062416_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA14G02210.1 (Glycine max), 5'ss of exon 8
GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtacttttaacttgatttgtttccagaaggttacacatttattggtggtgattttgaatgggttaa-atcaatttctgaatgtacctgctagtttgt------
|| ||||| || || |||||||| ||||||||||||||||| || ||||||||||| || ||  ||  ||  | ||| | | |     ||  |   | ||  ||  |      | ||||| || ||  |   | ||| | ||  || |   |  || |      
GACTTTGGTGATAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAGgtttg--ctcatagatagatatttatgtgctagaattatccttggtttata-----tctgaataggctattacttaattcaggatacacttttcacattttttattg

upper sequence: GRMZM2G062416_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G46440.1 (Glycine max), 5'ss of exon 10
GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtacttttaacttgatttgtttccagaaggttacacatttattggtggtgattttgaatgggttaaatca-atttctgaatgtacctgctagtttgt----
|| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| || ||  | |  |  || || |  |   | |||  |   | ||  ||  |      | ||||| || ||  ||  | ||  | ||  || |   || || |    
GACTTTGGTGACAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAGgtttgctcatagatatttatgtactagaataagaattatccttggtttata-----tctgaataggctatttctcaattaaggatacactttacagattttttat

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|71429076|gb|DR810126.1|DR810126
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|211157823|gb|FL476882.1|FL476882
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|71770625|gb|DR968562.1|DR968562
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|211031482|gb|FL468605.1|FL468605
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|32908945|gb|CF013758.1|CF013758
EST:     GGGACAGCATACCAGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|71324038|gb|DR798706.1|DR798706
EST:     GGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|71770099|gb|DR968036.1|DR968036
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
EST: gi|24773898|gb|CA409152.1|CA409152
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTTGCGTACATCTATTACCAATC
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTT-GCGTACATCTATTACCAATC
EST: gi|78074248|gb|DV502682.1|DV502682
EST:     GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAA                         ATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA
genomic: GGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtactt ... tatcttgcagATGGTCATGGCTGTTTTTGCGTACATCTATTACCAATCATTTGTAATGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGGGGACAGCATACCTGGTCATGGTGGATTTACAGATAGGATGGACTGCCAAgtatgtacttttaacttgatttgtttccagaaggttacacatttattggtggtgattttgaatgggttaaatcaatttctgaatgtacctgctagtttgt

- - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - GATGGA