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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag

Basic information

species Zea mays
transcript GRMZM2G370332_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 5'ss of exon 4
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatata-attccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag
||||||  | |||||||| |||||||| ||||||||||| |||||||||||| | || ||||||||||||||||||||||| ||||||||||||||||||||| ||| ||| |      ||| |   |  | |  | |  || || |||||  |  || ||||  | || | | |||||    |   || |||
AGAGATCCTTCGCAAGCGGAGAGCTGGTAAACTTCCTGGTGATACTGCATCTATACTAAAAGCTTGGTGGCAAGCTCATTCTAAGTGGCCATACCCAACTgtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcatgac-gagcaattctttctacacatattcag

upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G06890.2 (Glycine max), 5'ss of exon 4
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatataattccctcgtcaa-cttttgctatcagcttgggttca--ttgctgatccactctttgcttattcatccag------
 || ||| | || ||| |  ||||||||||||||||||| || ||  | ||||| || ||||||||||||||| | |||||||||||||| || || || ||| |  || | |        |||  ||   | |  || |  || | | ||  || |    |  ||  |||   ||        | | | |  |       
GGAAATTTTACGTAAGAGACGAGCTGGGAAACTTCCTGGTGACACGACCTCTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTATCCTACGgtaag-aactcaagactttactatgtttttttaggaaatccctttcaaacaaatttgaacgaatttaatgaataacaacaaagatgtccttgtacatattt

upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 5'ss of exon 5
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgt------gacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttca--ttgctgatccactctttgcttattcatccag
 || ||| | |||||| |  ||||||||||||||||||| || ||  | ||||| || ||||||||||||||| | |||||||||||||| ||||| || ||| |       |||  |||  |    | |  ||| |     | | ||| | | ||  || |    |  ||   ||    |        |   | |  | 
GGAAATTTTACGCAAGAGACGAGCTGGGAAACTTCCTGGTGACACGACCTCTGTCCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCCACAgtaagaacccaagactttactacattttttttttctcagtaaacccttttcaaacaaatttgaacgaatttaaagaatagcaacaaagatgaccttgtac

upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G32980.2 (Glycine max), 5'ss of exon 4
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag-----------
 || ||| |||||||| | ||||| |||||||||||||| || ||  | ||||| || ||||||||||||||| | |||||||||||||| ||||| || ||| ||   |  |    || ||  |||     | | |  |  |||| |  |     | |  ||   ||   | |   | ||||   | | |            
GGAAATTTTGCGCAAGAGAAGAGCAGGGAAACTTCCTGGTGACACAACTTCTGTTCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCTACCgtaagtttgataaataaga-attcaatgtgtacattacatcatgcttttggaaaaagct--tttaagaattatttgattcttaactaacgaagtccttgtaag

upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G13750.2 (Glycine max), 5'ss of exon 4
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgt------gacactacggcgacatata-attccctcgtcaactttt---gctatcagcttgggttcattgctgatccactctttgcttattcatccag-
 || ||  |||||||| | |||||||||||||||||||| || ||  | ||||| || ||||||||||||||| | |||||||||||||| ||||| || ||| ||       | |  |   | | |  || |||    | ||||  |||   |  |  |||||     |||   |   |||   || | ||| | ||  || 
GGAAATCTTGCGCAAGAGAAGAGCTGGGAAACTTCCTGGTGACACAACTTCTGTTCTTAAAGCTTGGTGGCAATCACATTCCAAGTGGCCTTACCCTACCgtaagtttgataaataagaactcaataagtacatttttacatcaagctttttgggaaaaagcttttaaacata--taggccaagtttggattaat-atttagt

upper sequence: GRMZM2G370332_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 5'ss of exon 8
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgaca----tataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag---------------------------------------------------------
 |||||  | ||||| ||  | ||||| || || ||||  |  ||| || | ||  |||| |||||||||||||| ||||| ||||||||||| || || ||||   | | | |  |   |    |  | | |     || | |  |||| |  | |   |||||       ||     |    ||||  ||  |                                                          
GGAGATCCTACGCAAACGGCGTGCTGGAAAGCTGCCTGAGGGAACTACAACAGTCTTGAAGGCTTGGTGGCAAGCACATTCAAAGTGGCCATATCCCACGgtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttcacgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccag

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|71330383|gb|DR801947.1|DR801947
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|32868323|gb|CF008005.1|CF008005
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|71330382|gb|DR801946.1|DR801946
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|60397901|gb|DN230717.1|DN230717
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|93280940|gb|EB673204.1|EB673204
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|31611855|gb|CD568477.1|CD568477
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|32868033|gb|CF007715.1|CF007715
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGATTATGCGCAAGCGCAGAGCTGGGAAACTTCCTGGAGATACTGCATCTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA