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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtactagtgacagatgaccttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag

Basic information

species Zea mays
transcript GRMZM2G439457_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 6
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtactagtgacagatgacct-tatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag
 |||||||| ||||| || ||||||||||||||||| ||||||||||||||||| || || |||| |||    |||  ||  | | |  |   | |  | |   || || |   |  |||||   |||||  ||||  || | |||||||
GTTCATTTCGGTGCCCAAGGACATGGGAGCATTCAATTGTGGAGCTTTTGTTGCAGGAATCGTAAGGgtgaggattttagcccaaatatctattcatgtatgatatattctgagattaatattctaacatggctttaaaaatgtttgtag

upper sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G34840.1 (Glycine max), 5'ss of exon 7
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagt-------actagtgacagatgaccttatcattttgttgaagcaatatgtcaacatta-ctttgtaactttttgtag----------
 ||||||||| | ||||| ||||||||| | || ||||||||||| |||||||| || || |||  ||||     |    |        ||| || || ||    ||||| | || ||  || ||  | | || | ||  |||||    |||  |            
ATTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGgtaagtgctttgctttgttcagctactgtcaaatag--ttatcttattcttagagaaagttctaaatagtagttttgttttgtttcattcatcaatgaag

upper sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G03480.1 (Glycine max), 5'ss of exon 7
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtac---tagtgacagatgacc--ttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag-------------
 ||||||||| | ||||| ||||||||| | || ||||||||||| |||||||| || || |||  ||||     |    |      ||| || |   ||   | |||   || ||  || ||  | | || | |  ||| ||  || ||  |              
-TTCATTTCTATCCCAAAGGACATGGGAACGTTTAACTGTGGAGCATTTGTTGCTGGAATAGTACGGGtaattgctttgctttgttcagtaactgtcaactagtaatctgattcttagagaaaggtctaaagagtggttt-tattttgtttcattcatcaatgaagg

upper sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 5'ss of exon 6
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtac--tagtgacagatgaccttatcattttgttg-------aagcaatatgtcaacattactttgtaactttt-tgtag
 ||||||||  | ||||||||||||||| |||||||||| ||||| |||||||| ||||| || |||||      |||  |    || | ||  ||    ||   ||||  |||       ||| |     | | | | ||   ||  | | | |||||
GTTCATTTCGATTCCAAAAGACATGGGAACATTCAACTGCGGAGCGTTTGTTGCTGGCATAGTGAAGgtgagtgctcccttgacatattcacgaatagggttcaaatttaattggtagaggaagaagataatgagcctgacacggtttcctctatgtag

upper sequence: GRMZM2G439457_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 5'ss of exon 6
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtactagtgacagatgaccttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag------
 || || ||  | || |||||||||||| ||||||||||||| || |||||||| |||||||||| ||||   |      |  |  | ||  || | ||   | | | ||    | ||  | | |  |  | ||| ||  ||||| |        
ATTTATCTCAATACCGAAAGACATGGGAACATTCAACTGTGGTGCATTTGTTGCTGGCATTGTAAGGgtatgtaccatgtttgtttttactaattatctgtacttctggtcattgaaagctctgacaaacagtttttatttttttctctttgaag

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|211013166|gb|FL234108.1|FL234108
EST:     AAGACATGGGAGCATTCAACTGKGGAGCTTTTGKTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTT
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTT
EST: gi|32929722|gb|CF034534.1|CF034534
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|22520635|gb|BU079446.1|BU079446
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|78543983|gb|DV621481.1|DV621481
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|20512936|gb|BQ280122.1|BQ280122
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|21760153|gb|BQ635694.1|BQ635694
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGC
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGC
EST: gi|14701539|gb|BI233957.1|BI233957
EST:     CTGTGGAGC-TTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: CTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|78025988|gb|DV494375.1|DV494375
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|211436242|gb|FL480988.1|FL480988
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|74234989|gb|DT642903.1|DT642903
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|12971087|gb|BG267308.1|BG267308
EST:     ATGGGAGCATTCAGCTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: ATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|60395154|gb|DN228023.1|DN228023
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|149090503|gb|EE179813.2|EE179813
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|32866521|gb|CF006203.1|CF006203
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|149090504|gb|EE179814.2|EE179814
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|23357590|gb|BU645239.1|BU645239
EST:     CTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: CTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|5124235|gb|AI745971.1|AI745971
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|149071934|gb|EE160321.2|EE160321
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTTGT
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTT-GT
EST: gi|60346326|gb|DN213299.1|DN213299
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|74234990|gb|DT642904.1|DT642904
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|60355461|gb|DN222434.1|DN222434
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|71424450|gb|DR806314.1|DR806314
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|87157228|gb|DY402017.1|DY402017
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACAT
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACAT
EST: gi|211167228|gb|FL234178.1|FL234178
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCG
EST: gi|60399125|gb|DN231939.1|DN231939
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|32866520|gb|CF006202.1|CF006202
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|37382943|gb|CF628443.1|CF628443
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|60341828|gb|DN208801.1|DN208801
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|60348498|gb|DN215471.1|DN215471
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|21432407|gb|BQ547897.1|BQ547897
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|149071933|gb|EE160320.2|EE160320
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
EST: gi|20512935|gb|BQ280121.1|BQ280121
EST:     AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAG                         GGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG
genomic: AAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattc ... ctttttgtagGGTGTATTAGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCATTTCTGTGCCAAAAGACATGGGAGCATTCAACTGTGGAGCTTTTGTTGCGGGCATTGTAAAGgtagaaattccagtactagtgacagatgaccttatcattttgttgaagcaatatgtcaacattactttgtaactttttgtag

- - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - -  GAGCTT