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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccctccttaacctatatacttgaacaatgttatctacctttacttccagaaactttagcatgttatatgccttagccttcgatgcaatctctt...

Basic information

species Zea mays
transcript GRMZM5G813143_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 5'ss of exon 4
CCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccctccttaacctatatacttg----aacaatgttatctacctttacttccagaaactttagcatgttatatgccttagccttcgatgcaatctctt
||||| |||| |||||||| ||  | ||||| || || |||||| |||||||||| ||||||||||| |||||||||||||| ||||| ||  | |||||||||||   ||    |    |||||||||    | || | |||     ||||| || ||| || |  |     ||  |||  |  |       | ||       
CCATTAGACGAGCACATGCAGTTTACCCAATCACCGCAGTGCAGATGGAGTGGTCTCTATGGACCAGGGATATAGAGGAAGAAATAATCCCGCTGTGCAGgttcatgtactttcaatttcatatacttgttacagcatttttactctactttagttgcaggaaatacaagtacttgcatgtttctgaaagtagtacagca----

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA03G40680.1 (Glycine max), 5'ss of exon 4
CCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccctccttaacctatatacttgaacaatgttatctacctttacttccagaaactttagcatgttatatgccttagccttcgatgcaatctctt-
| ||| |  ||||||||||||| ||||| |||||||| |||||  |||||||||| || |||||  | || || ||| |||||||  ||||| | ||||||| |||        |   | |||   |  ||   ||||          | || | ||    ||  |   ||    | | ||        |  ||  |    
CAATTAGGAGGGCACATGCTGTTCATCCCATTACTGCTGTGCAACTGGAGTGGTCCCTTTGGACTCGTGAAATTGAGCAAGATATTGTTCCACTTTGCAGgtacataaagagggtg-tccataatgtaaaatgttgtttctgtggagaatttgctgatttgtttcctgcttcccagtcataattgagtttataagtttaga
















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|78114483|gb|DV532872.1|DV532872
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|74244513|gb|DT652427.1|DT652427
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|88756482|gb|DY540623.1|DY540623
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91873437|gb|EB403394.1|EB403394
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|89755225|gb|DY685734.1|DY685734
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGGCTTCT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGG-CTTCT
EST: gi|88757821|gb|DY541962.1|DY541962
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|76021184|gb|DT948354.1|DT948354
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|76021183|gb|DT948353.1|DT948353
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91875442|gb|EB405399.1|EB405399
EST:     GAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGC-TGGTATTGGAATAGTTCCATATAGCCCACTGGGCCGTGGCTTCTT
genomic: GAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|78114482|gb|DV532871.1|DV532871
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|78085303|gb|DV513696.1|DV513696
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|89761100|gb|DY689250.1|DY689250
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|76288052|gb|DV027620.1|DV027620
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91055988|gb|EB166406.1|EB166406
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|76288051|gb|DV027619.1|DV027619
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91877299|gb|EB407256.1|EB407256
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|101392432|gb|EB818145.1|EB818145
EST:     ATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCGTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: ATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|89755224|gb|DY685733.1|DY685733
EST:     AGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: AGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|76011255|gb|DT938425.1|DT938425
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|60355056|gb|DN222029.1|DN222029
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91873436|gb|EB403393.1|EB403393
EST:     AGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: AGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|74244046|gb|DT651960.1|DT651960
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|78112031|gb|DV530427.1|DV530427
EST:     GAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: GAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|89762828|gb|DY690268.1|DY690268
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|89761102|gb|DY689251.1|DY689251
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|78087084|gb|DV515477.1|DV515477
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|60341512|gb|DN208485.1|DN208485
EST:     GTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: GTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|101392434|gb|EB818146.1|EB818146
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
EST: gi|91875443|gb|EB405400.1|EB405400
EST:     TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAG                         GGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT
genomic: TGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccc ... ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATTCGACGGGCACATGCTGTCCATCCAATTACTGCGGTGCAGTTGGAGTGGTCACTATGGACCAGAGATATAGAGGAAGATATAATTCCAGTCTGCAGgttcatcccctccttaacctatatacttgaacaatgttatctacctttacttccagaaactttagcatgttatatgccttagccttcgatgcaatctctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG