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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatggttttgcctcactttattcttgctgtagattgtttgcttgtcgctttcatggagcgtgtctgtgggtacttttgcttgcccgcttgcatttatgtcgtgctgctgttgcttgccattcag

Basic information

species Zea mays
transcript GRMZM2G107106_T07
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T07 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g41010.7 (Oryza sativa), 5'ss of exon 3
GGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatggttttgcctcactttattcttgctgtagattg--tttgcttgtcgctttcatggagcgtgtctgtgggtacttttgcttgcccgcttgcatt-tatgtcgtgctgctgttgcttgccattcag
||||||||||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||||  |||||||| ||||||||  | ||  | |||||||||     |    ||         || ||  || ||||   |  |||  |||   |  | |    |  ||    || || |||| | | | |  | |   ||||  |                       
GGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCCCACCGACTATACGgtacatgtgattgccaccgatgcgcgctcatgtggttgattagttccgctcatcgtgatttttgcatttacctagtcgtgctgttgcctcctctccagaaggatatgcag-----------------------

upper sequence: GRMZM2G107106_T07 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g41010.2 (Oryza sativa), 5'ss of exon 3
GGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatggttttgcctcactttattcttgctgtagattg--tttgcttgtcgctttcatggagcgtgtctgtgggtacttttgcttgcccgcttgcatttatgtcgtgctgctgttgcttgccattcag
||||||||||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||||  |||||||| ||||||||  | ||  | |||||||||     |    ||         || ||  || ||||   |  |||  |||   |  | |    |  ||    || || |||| | | | |  |                                  
GGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCCCACCGACTATACGgtacatgtgattgccaccgatgcgcgctcatgtggttgattagttccgctcatcgtgatttttgcatttacctagtcgtgctgttgcctcctctccag----------------------------------

upper sequence: GRMZM2G107106_T07 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 5'ss of exon 3
GGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatggttttgcctcactttattcttgctgtagattgttt--gcttgtcgctttcatggagcgtgtctgtgggtacttttgcttgcccgcttgcatttatgtcgtgctgctgttgcttgccattcag
||||||||||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||||  |||||||| ||||||||  | ||  | |||||||||     |    ||         || ||  || ||||  ||  |||  |||   |  | |    |  ||    || || |||| | | | |  | |                                
GGACGACTGGGTTTGCCCCAGCTGCCAGAACGTCAACTTCGCCTTCCGCACCACCTGCAACATGCGCAATTGCAACCAATCCAGGCCCACCGACTATACGgtacatgtgattgccaccgatgcgcgctcatgtggttgattagttccgctcatcgtgatttttgcatttacctagtcgtgctgttgcctcctctccagaag-------------------------------

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|71439479|gb|DR820529.1|DR820529
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|22819789|gb|BU499879.1|BU499879
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|74243877|gb|DT651791.1|DT651791
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         --G-CCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|87157437|gb|DY402226.1|DY402226
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|31353283|gb|CD437640.1|CD437640
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|78115667|gb|DV534055.1|DV534055
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211345683|gb|FL376446.1|FL376446
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|26559278|gb|CA831513.1|CA831513
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211157842|gb|FL370480.1|FL370480
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|37418046|gb|CF646683.1|CF646683
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|87157624|gb|DY402413.1|DY402413
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|148973713|gb|EE024841.2|EE024841
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         --G-CCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211219381|gb|FL389590.1|FL389590
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|148947916|gb|EC893413.2|EC893413
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211506959|gb|FL409459.1|FL409459
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|26559761|gb|CA831996.1|CA831996
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|71446967|gb|DR828017.1|DR828017
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACAC-                         --GGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|22542254|gb|BU092692.1|BU092692
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211479168|gb|FL394817.1|FL394817
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|71313389|gb|DR793245.1|DR793245
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACAC-                         --GGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|71765408|gb|DR963345.1|DR963345
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACAC-                         --GGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|37417359|gb|CF646332.1|CF646332
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         --G-CCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|74238077|gb|DT645991.1|DT645991
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACAC-                         --GGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211379109|gb|FL373375.1|FL373375
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|71439462|gb|DR820512.1|DR820512
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC
EST: gi|211019422|gb|FL374992.1|FL374992
EST:     CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACG                         AAGGCCATGCAGACCCCGCCTCACTATCCCATGTCAGGGGGTTACATGGGC
genomic: CCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatg ... tgccattcagAAGGCCATGCAAACCCCGCCTCACTATCCCACGTCAGGGGGTTACATGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACGACTGGGTTTGCCCCAGCTGCAAGAACGTCAACTTCGCCTTCCGCACCACTTGCAACATGCGCAGCTGCAACCAGTCCAGGCCAGCAGATCACACGgtacataatggttttgcctcactttattcttgctgtagattgtttgcttgtcgctttcatggagcgtgtctgtgggtacttttgcttgcccgcttgcatttatgtcgtgctgctgttgcttgccattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA