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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctagataaagctattgttgacttgaaatcttactttgttgctgaaattgcctaaggaaaa...

Basic information

species Zea mays
transcript GRMZM2G012319_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012319_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 17
AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctaga----taaagctattgttg-acttgaaatcttactttgttgctgaaattgcctaaggaaaa----
|||| |||||||||||||| ||||| ||||||||||||||||| || || || |||||||||||||||||||| || ||||||||  | |||||||||||||||||         || | | ||   |||   | || | ||| |    |||| |||||  || | |  |||  |||| || |||||  || ||| ||| |  |     
AACTTAAGAAACTTTATGAGACCCACGAGAGGCTTCTTGATTTCGTCTCTTTGTTCTGTTTTGTTCCAAGGGCCAAGTACTTGCCTTTAGGTCCTACCAGgtatgt---------gtcaatctttgggggttctaatctcctaaagcagtaaaactattcctggattcaaaaggttaccttattgctacaactgcttaaagttagacct

upper sequence: GRMZM2G012319_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA05G36530.1 (Glycine max), 5'ss of exon 19
AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctagataaagctattgttgacttgaaatcttactttgttgctgaaattgcctaaggaaaa----
|||| |||||||| |||||||||||||| ||||| || ||  ||||||| || || |||| |||||||||  | || ||  | ||  | || || |  ||||||  |   |  ||   | | |  |   | | | |||||  |  | |  |   |  |  ||  | |   || | || |  |     ||| ||  | | |    
AACTGAAGAAACTATATGAAACCCATGAAAGGCTGCTAGACCTTGTTTCATTGTTTTGTTATGTTCCAAGAACAAAGTATCTACCTTTGGGCCCAATAAGgtattgatatttaattgcattctgtattcgaactaattttgcatgttactcatgttgtatctaaagagactagtatgctctt----ctgcatacaggagagtgc

upper sequence: GRMZM2G012319_T02 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA08G03020.1 (Glycine max), 5'ss of exon 19
AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctagataaagctattgttgacttgaaat--cttactttgttgctgaaattgc--ctaaggaaaa
|||| |||||||| |||||||||||||| ||||| || ||| ||||||| || || |||| |||||||||  | || ||  ||||  | || || |  ||||||  |   |  ||  || | |    |    |    | |    ||   | | | | | || |||  |   ||    | || || |  |||   |||| ||  |
AACTGAAGAAACTATATGAAACCCATGAAAGGCTGCTAGATCTTGTTTCATTGTTTTGTTATGTTCCAAGAACAAAGTATCTGCCTTTGGGCCCAATAAGgtattgatattgaattgaattct----gtatttgagctcttagaatgtgggtttgggttacatgaggtaattttgcatattactcatgttgtatctaaagagga

upper sequence: GRMZM2G012319_T02 (Zea mays), 5'ss of exon 18
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 5'ss of exon 20
AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctaga--------taaagctattgttgacttgaaatcttactttgttgctgaaattgcctaaggaaaa
|||| |||||||| |||||||||||||||||| | || ||| |||||||  | || |||| ||||||||| || || ||  | ||  | || ||||  |||||     |    ||   |  |  |||    || || ||| | ||        ||    | | |||||  || || || ||    |     |  ||   | | |    
AACTTAAGAAACTGTATGAAACCCATGAGAGGTTGCTAGATCTTGTTTCACTGTTTTGTTATGTTCCAAGAGCGAAGTATCTACCTTTGGGGCCTATAAGgtacacttt---catcctataagaaaaaaaaatacactttttggagtgcattttatctttctagttgatgtggaa-ctaacgacatcctgtattttattttaag----

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|60347368|gb|DN214341.1|DN214341
EST:     TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAG                         TGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
genomic: TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtacta ... gtatggacagTGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
EST: gi|60340403|gb|DN207376.1|DN207376
EST:     TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAG                         TGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
genomic: TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtacta ... gtatggacagTGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
EST: gi|76909472|gb|DV163397.1|DV163397
EST:     TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAG                         TGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
genomic: TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtacta ... gtatggacagTGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
EST: gi|89251966|gb|DY623752.1|DY623752
EST:     TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAG                         TGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG
genomic: TTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtacta ... gtatggacagTGCCAAGCTAATTGAGATCTACCGCAACCGTCATAACATAAGTGCTTCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTCAAGAAACTTTATGAAACCCATGAGAGGCTTCTTGATTTTGTTTCCTTATTCTGTTTTGTTCCAAGGGCTAAATACTTGCCCCTTGGTCCTACCAGgtatgtactatatatgtaactattaaagggcattcattttctagataaagctattgttgacttgaaatcttactttgttgctgaaattgcctaaggaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agataaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaggaaa