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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACCATCTTCTGGGTGGGAGAGTGGTTTATAAAGAAAATGCCATTTGTAAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagcatccattgcatgtgtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttag

Basic information

species Zea mays
transcript GRMZM2G046098_T05
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046098_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 5'ss of exon 3
TCAACCATCTTCTGGGTGGGAGAGTGGTTTATAAAGAAAATGCCATTTGTAAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagcatccattgcatgtgtttctt---tttttatattttaa--agatagtttgcacaa--gaagttttcttatgtaattattttgtt-gttag
||||||||||| ||||| ||||| ||||||||||||||||||||||||||  |||| ||||| || || |||||||||||||||||||| ||||||||||||       ||| ||    || | ||  |      || | | | | |  ||  |  ||| ||||  ||| ||  || ||  ||| || ||||| |  ||
TCAACCATCTTTTGGGTTGGAGAATGGTTTATAAAGAAAATGCCATTTGTTCGGCACATATACTCTGCATCAAAGCAAGTCAGCACTGCCATTTCACCAGgtatacttccatacacaa-atatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcag

upper sequence: GRMZM2G046098_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 4
TCAACCATCTTCTGGGTGGGAGAGTGGTTTATAAAGAAAATGCCATTTGTAAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaa-gcatccattgcatgtgtttctttttttatattttaaagatagtt------tgcacaagaagttttcttatgtaattattttgttgttag--
 | ||  | |||||| | ||||| ||||||||||||| |||||| ||||| | ||||||||| || || || |||||| | ||  | |||||||| |||||| |     | |    ||  |  | |||  ||    |  ||  |    |||||      |||| ||  | ||   ||||| |  ||  |||   ||    
GCCACTGTTTTCTGGCTTGGAGAATGGTTTATAAAGAGAATGCCCTTTGTTAAGCATATATACTCGGCCTCCAAGCAAATTAGTGCCGCAATTTCTCCAGgtaactcctgaagtttttttacatttttgcttaccgactttcaacgcctagttgtttggtgcaaaaatacttgcattatgaacataaattgaaatttctg
















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|51871157|gb|CV126041.1|CV126041
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|211391866|gb|FL013594.1|FL013594
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAGAATACGACAGCTTTTCAAAGAAAGCTGCA-TAATTCGTCATCCACG
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTT-CAAAGAA-GTTGCAATAATTCGTCATCCACG
EST: gi|91053372|gb|EB163790.1|EB163790
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|50323815|gb|CO518941.1|CO518941
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|88755429|gb|DY539570.1|DY539570
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTT
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTT
EST: gi|74239462|gb|DT647376.1|DT647376
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|60398318|gb|DN231134.1|DN231134
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|28910665|gb|CB331552.1|CB331552
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGAC
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGAC
EST: gi|76293651|gb|DV033219.1|DV033219
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|148944675|gb|EC889811.2|EC889811
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|40287192|gb|CK327584.1|CK327584
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|148949550|gb|EC895017.2|EC895017
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACCATCTTCTGGGTGGGAGAGTGGTTTATAAAGAAAATGCCATTTGTAAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagcatccattgcatgtgtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG