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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat...

Basic information

species Zea mays
transcript GRMZM2G443985_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatat---acgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat--
||||| |||||||| |||||||||||||||||||||||||| || |||| ||| || |||||||||||||| || || |||||||||||||| |||||||||| | ||||  |  |     |||  |  ||||   ||   ||  |||  | | |  ||||   |   | |||| |  |       |   ||||| |||||||  
GCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAGGCCTCGTAAAGCTAATGGGTCGACACAGTGgtatgtttcttggccacagtgatatgtcgtgctggaatgaaacattattagcccatcatatacttaggtcaattcagca-----caatagtttctatgctaatat

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA05G36050.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgaga-----ggcgaataaatta--tgctaatatacgatatctgtcaaatatat-gtgtcaattaattaactaactcttga-gtatttctctgctaat
|| || ||||||||||||||||| |||||||| || ||||| ||||||| ||||| ||| ||||| |||||| |||| ||  | ||||| ||| ||||||||||| ||||   |          ||  | ||||     ||  || |  ||  |     | ||||  ||| ||||| ||   | |  | ||  | ||    | |     
GCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAGGTGTTGTTAAATTGATGGGCCGGTACAGTGgtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcattgacatattatgttaattattttcttgatacatggtgcatggtgcag-----

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G03570.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgaga-----ggcgaataaatta--tgctaatatacgatatct--gtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat-----------
|| || ||||||||||||||||| |||||||| || ||||| ||||||| ||||| ||| ||||| |||||| |||| ||  | ||||| ||| ||||||||||| ||||   |          ||  | ||||     ||  || |  ||  |    |||  | || | |   ||||| || ||  |  |   | |   | |    ||           
GCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAGGTGTTGTTAAATTGATGGGCCGGTACAGTGgtaagtttcttgaatgcctccactgatcagattaatcattagcatcctgtacttcaaccaatgacatat-tatgttaataaattattttctcgatgtaattatatggatgcatggtgcag

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G01710.1 (Glycine max), 5'ss of exon 8
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcg--aataaattatgctaatata---cgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || || ||||| ||||| || |||||||||||||||||||| || | |||  ||||||||||||| ||| |||||||| |||||||||| ||||||||||||  ||    | |      |||  |  || | |   ||    |||    || | ||| |   |   ||     |  | ||   | ||   | || || |   
GCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTGGTGTTGTCAAGTTAATGGGTCGTCACAGTGgtaagtatcatttatatttcgtaatttacaatacaagcttagcctgatggaagttatatagagtagaagatctgaaagatgacctgtaag--ctgctgtgat---

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G02400.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttc-tacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat-------
|| || || ||||| ||||| ||||| ||| ||||||||||||| || | ||| || |||||||| || ||| |||| ||  ||||||| ||  ||||||||||||||| | |      |  |||| |||    ||  |  ||  ||  |  | | | | | |||  | |  | ||  ||| | ||  |||| |     |        
GCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTGGTGTTGTAAAATTAATGGGGCGTTACAGTGgtaagcttcattcattcctctgataatttac---aactttagagttccat--actttttctttca--tgac-atcttcctccttagagtttcccataggagacctgtc

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G09180.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat-
|| || ||||||||||||||||| || ||||| |||||||| || |||| ||||  |||||||||||| ||| |||| ||||||||||| ||  | ||||||| |  |     | |   |  | |  | |  ||     | |  ||  |   |  | | | ||||| |     ||  || |||    |   |   ||||  
GCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTGGTGTTGTAAAGCTAATGGGGCGTTATAGTGgtatgtatacttcacatttgtttgatatcttttaggcatctaattcacttttagctctct-tcaatcaggcttctgtcttttggagttggtttctctaaag

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G42990.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttc-tacgagaggcgaataaattatg-ctaatatacgata--tctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || || ||||| ||||| ||||| ||| ||||||||||||| || | ||| ||||||||||| || ||| |||| ||  ||||||| ||  ||||||||||||||| | |      |  |||| ||    || |  | | |||  | |||  |||       |   | | |||  |     || |  |  |||        
GCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCTGAGAATGGAATTGGTGTTGTAAAATTAATGGGGCGTTACAGTGgtaagcttcattcattcctctgataattttcaacttaagttccatacatatgttgaatgctgacctttgtcacttactttttctttcatgacatcttcct----

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G21370.1 (Glycine max), 5'ss of exon 8
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcg--aataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || || ||||| ||||| || |||||||||||||||||||| || | |||  ||||||||||||| ||| ||||||| ||||||||||| ||||||||||||  ||    | |      |||  |  || | |   ||   | | ||  |  |||||     |    ||     |  |     |||     |||  |  
GCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATCGGTATTGTCAAACTAATGGGTCGTCACAGTGgtaagtatcatttatatttcgtaatttacaatacaagcttaacct-tatgctagctatatagagtagaagatctgaaagatgacttgtaagctgctgtcat-

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G09320.1 (Glycine max), 5'ss of exon 8
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagc---ttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || ||||||||||||||||| || ||||| |||||||| || |||| ||||  ||||||||| || ||| |||| ||||||||||| ||  ||||||||| ||    | | |    |    |||  || |    || ||    |  ||    | |    | |   ||       || ||||     ||    || ||   
GCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTGGTGTTGTAAAGCTAATGGGACGTTACAGTGgtatgcatactttgcatttgcttgatatcttttaggcatctaattcagatgattgaaacccttttatgtttcacttttagctctcttcaatcgggcttct---

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G00870.1 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaa-ttaactaactcttgagtatttctctgctaat-----
|| || |||||||||||||| || |||||||| || ||||| || |||| |||||  || ||||| |||||| |||||||| | |||||| |  |||| |||||| |||  | | | ||  ||||    ||||   |  |  |  ||      |  |  | | || ||  || |  | |    || || |     | | ||     
GCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCGgtaagtttc--ctaaatgcttataa----tgcttccactcactggcttaagggttcaatttttaactatcttcaacagcctaagaataatgagaagtttatatctt

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA07G15170.4 (Glycine max), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaa-ttaactaactcttgagtatttctctgctaat-----
|| || |||||||||||||| || |||||||| || ||||| || |||| ||||| ||| ||||| |||||| |||||||| | |||||| |  |||| |||||| |||      |   |  ||||  |||||   |  |  |  ||      |  |  | | |||||  || | || |    || || |     | | |      
GCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTTGAAAATGGCATAGGTGTTGTCAAGTTGATGGGTAGAAACAGCGgtaagtttcct----aaatgcttaaa--atgcttccactcactggcttaagggttcaatttttaattaccttcaatagcctaagaataatgagaagttcacacatc

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || || |||||||||||||| || ||||| || ||||| || |||  |||   |||||||||||| |||||||| ||| ||||||| ||| |||| ||||||    | |   || |   | |  || | |   |  | |  |  |   |  |     |   |    || ||  | |||| ||  ||| |        
GCTGTAGAAGAGGCTCAACGTGCTATCAATGCAGCACATGTCGAAGCTACAAGCTTTGAGAATGGTATTGGTCTTGTGAAGTTAATGGGACGGTACAGCGgtaagaagtttccctagac---ttaggta-gttttcacccaagtttagctgagcac---cgaagagatgtttacggattcttaagggtttgtgcag----

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 5'ss of exon 9
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacga-tatctg-tcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat------------------
|| || ||||||||||||||||| || ||||| || ||||| || ||    ||||  || || || || ||  |||||||||||||||||||| ||||||||||| |   |  |||  | |  | |  |       |||| | |||  |  || | |  | | |   |||      ||   | |  |  ||| |||  |  |                  
GCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTGGAATTGTCAAGCTAATGGGTCGGTACAGTGgtaagttcacagaagaatctaggagagcagtaatgcatacaaatattagaccacagaagtatcttctttatgatgttactccctacgcttttatctaatcttacagcttctacactgcag

upper sequence: GRMZM2G443985_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT5G56630.1 (Arabidopsis thaliana), 5'ss of exon 7
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat
|| || ||||| |||||||| || || || || || ||||| || || |  |||  |||||||||||| ||| |||||||||| ||||||||  |||| ||||||  | |            | ||  || | ||  ||  | | || |   || | | |    | ||||   |||      | || ||   || |    
GCTGTGGAGGAAGCTCAACGAGCGATTAACGCAGCACATGTTGAAGCCGAGAGTAATGAGAATGGTATCGGTTTTGTCAAGCTTATGGGTCGTTACAGCGgtaagtctttgttt--------tgaaacatac-aacttaaaagaccttttcgatttgt-tactgactaat--gctagg---cgggtgttgtactacag--

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|32938375|gb|CF043194.1|CF043194
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|32938968|gb|CF043787.1|CF043787
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|488227|gb|T18808.1|T18808
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|32939806|gb|CF044625.1|CF044625
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|32939493|gb|CF044312.1|CF044312
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
EST: gi|211132969|gb|FL170874.1|FL170874
EST:     AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTG                         GTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG
genomic: AAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttct ... actaatgcagGTTTTATTGCACATTATGCTACTCTGGCTAGCAGGGACGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGTCGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAGGCTGTAAGTGCTGAGAATGGTATAGGTCTTGTCAAGCTAATGGGTCGGCACAGTGgtaagcttctacgagaggcgaataaattatgctaatatacgatatctgtcaaatatatgtgtcaattaattaactaactcttgagtatttctctgctaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT