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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag

Basic information

species Zea mays
transcript GRMZM2G181151_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
|||| ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||| |||||||| |||||||||||||| ||||  ||| | || | || |||||| | | ||  || |      |   |   | ||       |  || |||    |  | |  |||      |  | |||   ||  |   ||||   |   | | | | ||||   ||||||  |||  || |   ||||  | | |                     
ATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttcttttctgttcttttattgagt-agcaaagattttcttggtaagagtaactggc------tgcttcatactccacctcaatatta-----tgacacatgaatgtaacttaata--gatcttctatattttttactctacctcaatattttct---tgttactttcag--------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgt-tataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
 ||| || || |||||||| || ||||| ||||| |||||||||||||||||||| || || || ||| |  ||||||| ||||||  ||  ||     ||| |   ||   ||  |||||| || |     |  |  | ||   |  ||||||| || ||   ||||| |       ||  |  |                                                                                            
-TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtca---cctgaattatgtacaaaagaatttggtgcagaataaatctta-------------------------------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA09G38110.1 (Glycine max), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggt-ctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
|||| ||||| |||||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||| |  ||||||| ||||||  || |||||    || |   ||   ||   ||| || ||        || |  ||   |  ||||||| || ||   ||||| |       ||  |  |                                                                                            
ATATTACACATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATTGACAGGCAGTTGTATAACAGGCAGgtgggtt-ctttgaagattttggctgctgta---aatattgtataaaatgctgggttagtcacctgaattatgtacaagagaatttggtgcagaataaatctta-------------------------------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G42940.2 (Glycine max), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaa--atttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
|||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| |||||||||       || | ||  |   || || |   |||||    | | |   || |  || ||   | |||| ||| ||   |  |||| |||     |   | || | |||| | ||                                                                                
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtggg-----ttatgttgaagctttcagctg--taatg----aacattgtatac--caagtt--ggattagttacaagagagaatttggcaaagaatgcatcctaacatttta-at--------------------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G24070.2 (Glycine max), 5'ss of exon 12
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaa--atttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
|||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| |||||||||  |     | | ||  |   || || | |  ||||  | |  ||      |  || ||  |  |||| ||| ||   |  |||| |||         | || | |||| ||                                                                                  
ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAGgtgggt-----tatgttgaagctttcagctgt--aatga-acatttt-----acaccaagttcg--attaattagaagagagaatttggcacagaacgcatcctaacatttaatg---------------------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
||||||| || ||||||||||| |||||||| ||||||||||| || |||||||| || |||||||| || || |||||||||||        |       ||    ||||    || || |||    ||    |     |  |   ||      | | | | ||| || | ||  || ||  || | |                                                                                        
ATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAGgtaa------taaataactaccgctgaggc-cctgatcttactggtttcagta----atattatgatccggctctgaatgaatgtatctttgtttcttccctgaaaaacag-----------------------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttc-tttgtcttttattcttgagttatctaatgttatacctt-cacatgcggca-ggtctggaattatttataactaaatttagcat---ttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||| || || |||||||||||||  |    | | ||||| | | |   |    | |||   |  ||  |||||    ||    |  |||   ||| | | || |||||  ||    ||| ||| | || |  ||  |    || |                                                                          
ATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAGgtgcaataagctcgacttttttgcatatatctcattatgagctctctaacacatcaaacataagcaagaaaggtttctca-tacatttacaatgatctctgattctgtcttggttcttccctaaaacag-----------------------------------------------------------------------

upper sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 11
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgctttt---ctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag
|||| || || |||||||| || |||||||| || ||||||||||| |||||||||||||||||||| ||||| ||| | ||||||  ||    |       ||| ||| ||    |    || || |  | || |    ||||  |      ||  |  | ||||  |  ||  || ||  ||||                                                                                              
ATATTACGCATCCAACTCCAGATCTTACTGGTTATATTACTGAGGGCCAGATATACATTGATAGGCAACTCCACAACCGGCAGgtgagttgaaaccaaactctttcttcatgttaaaatacatatt-tgtcatctctcatggcatatgcact-tttctcctgactacgtggagt-ttgctagtttt----------------------------------------------------------------------------------------------

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|60355003|gb|DN221976.1|DN221976
EST:     GGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: GGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|16925493|gb|BM078561.1|BM078561
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|32945219|gb|CF050038.1|CF050038
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|60343435|gb|DN210408.1|DN210408
EST:     GACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: GACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|60352479|gb|DN219452.1|DN219452
EST:     GGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: GGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|6973468|gb|AW438162.1|AW438162
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|67019767|gb|CO448516.1|CO448516
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|33101769|gb|CF061729.1|CF061729
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCCCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|194716931|gb|FK934090.1|FK934090
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|211222467|gb|FL437623.1|FL437623
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|60394888|gb|DN227757.1|DN227757
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|67015926|gb|CO444675.1|CO444675
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|33101431|gb|CF061391.1|CF061391
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGCCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|213188201|gb|FM181912.1|FM181912
EST:     AGGCAGCTCNNTAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: AGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|60395817|gb|DN228687.1|DN228687
EST:     TTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: TTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|24767815|gb|CA402951.1|CA402951
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCGTCTCTCTCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|32944615|gb|CF049434.1|CF049434
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|60396754|gb|DN229618.1|DN229618
EST:     GGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: GGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|37401251|gb|CF637988.1|CF637988
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|33094143|gb|CF054137.1|CF054137
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|32933748|gb|CF038560.1|CF038560
EST:     ACATTGCTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|32942169|gb|CF046988.1|CF046988
EST:     ATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|32931582|gb|CF036394.1|CF036394
EST:     ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: ACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
EST: gi|211222468|gb|FL437624.1|FL437624
EST:     CATTACTGGGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG                         ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG
genomic: CATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttct ... tttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC