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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact...

Basic information

species Zea mays
transcript GRMZM2G011518_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcat----aaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact
 ||||||||||||||||| |||||||| ||||||||||||||||||||||| ||  | |||||| | ||||||||||||||||||||||| ||||||||||||| |  | |  |  |   |||     |  ||||||||    |||   |  | | |  | |  |    | |   |      |        |||  |||     
AGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAACAACACCGATGCTCTGgtcactctttttttcccctcttcttttatccagcggcatagggaaacatttcttacacataacgtacctcctttgaacaagcaattcactttgtgacttt----

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G01380.2 (Glycine max), 5'ss of exon 4
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaag-ttgaaattttacatagaagtgtttatgctgtaatgtttctt-ccact-----------------------------------------------------------------------------
 ||||| || || |||||  | ||||| || ||||||||||| || || ||||| || ||||| || ||||||||||| || |||||||| ||||  ||||| |  | |    ||  ||  |   |  |   | |  | |||   ||| |  || |||   |||| |  | |  |  || |      || |   |   || |                                                                             
AGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAACAACACAGATGGCCTGgtgagaattagttttcatgccttttatctcg-gtgaaagaaaagttatgctgagcttgttgtttttcgaaaagttccttctttctccatatcattaatcagtccagtaggctggaaagaaaggtctacaggcacaaggtagcaaggttgatatatttgttgatgtgtgcatttatgcag

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G02110.1 (Glycine max), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtca-------ttactctcgttt-ctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagt--gtttatgctgtaatgtttcttccact--------------------------------------------------
|||||| || |||||||| || ||||| || ||||||||||| || || |||||  | ||| | || ||||||||||| || ||||||||||||| | |||| |       || |  |  |||  ||| |   |  | ||     | | |   | | |||  |||  || ||  | ||   |  || |||     |||  ||| ||   |                                                  
GGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAACAACACTGATGGTTTGgtaagaatgagtttccattatttgttgtgttttatcttaatgaaaacacaacttctgcaat-ttggtatcttgtaaagttttccgtctattacaaaatcattcatcacatgttacagatctatagttgccaggttgatacatatgtgcatatttatgcag

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G43910.2 (Glycine max), 5'ss of exon 4
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaa--agttgaaattttacatagaagtgtttatgctgtaatgtttcttccact-----------------------------------------------------------------------------------
 ||||| || ||||||||  | ||||| || ||||||||||| || || ||||| || ||||| || ||||||||||||||  ||||||| ||||  ||||| |  | |    ||  || ||       |  |    | || || | || |    ||||   |||||   | ||   |||      |      || |  |                                                                                     
AGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGACAACACAGATGGCCTGgtgagaattaattttcatgcttttatctcggtgaaagaaaagttatgttaagctggttgtttttttattaaaaaaaatttccttctttcaccatcattaatcagtccagtagaggcctggaaagaaaggtctacatgcataaggtagcaaggttgatatatttgttgacgtgtgcacttatgcag

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATG-----------CTCTGgtcattactctcgtt---tctgtttcacaagtgaagcggcataaattctattc------aaagttgaaattttacat------agaagtgtttatgct--gtaatgtttcttccact-----
 ||||| |||||||||||  | ||||| || ||||||||||||||||| |||||||| |||||| |||||||||| |||||||| || || ||||           ||||  | |||  || || |   |||  ||    ||| ||     | |   |||  ||      | || |||  | | |  |      || | | ||  || |   || || |   | || |     
AGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAATAATACCGATGGACTTgtaagtctctacttatttttcacgctgcctctagttagatagttaactcatagagtctcttctcttcatgacagatgatttctcatgttttgtaaggaattttcctgattgatattggtcgatgcatttgcag

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgt-cat---tactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttga---aattttacatagaagtgt-ttatgctgtaat-gtttcttccact----------------------------------------------------------------------------------------
 ||||| |||||||||||  ||||||| || ||||||||||||||||| ||||| || || || || |||||||| |||||||| || |||||||  || || | |   || | |  |||  | ||      |  ||    |||  |    ||||| |||     |  | ||  | |   | | |||| || || | | || |     |                                                                                        
AGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAATAATACTGATGGACTTgtacgtatatagtttttttttcgatttttgctttcagtcagatacttaactttcaaggtttttccatctctatgttggcatatgttatcctatatttggttatgatgttgcagtatcatatgttgcttggccaatctttagatctttttccatctttatcgaccatggtataagactactctatgatgctcttgcag

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttct-gtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact
 ||||| || ||||| ||  ||||||| ||||||||||| ||||| || ||||| |||||||| || |||||||| ||||| || || |||||||  ||||| || | |    ||| | |    |   ||   |        |||    |||   |     | ||  |    |  |||     ||||   ||         
AGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcattactttttatagccatatttgttcggtaattgttattagggtcagtttcattttattttaagttaccgttctctttgtataattctaaatgt-

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctc-----gtttctgtttcacaagtgaagcggcataaattctattca---aagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact
 ||||||||||||||||| | |||||| || ||||||||||| || ||||||||  |  ||||||| ||| |||| |||||||| || ||||| | | |||| | || |||      ||| ||||||||   ||  | |    |   || | ||||   || ||   ||  || ||| |  | | |||      || | | |      
AGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAATAATACTGACGGTTTGgtaagtattctttataggttgctgtttca---gtagacctttttttctttttttcatacaactttttatgatatatatatatatatatatatatatatatata-----

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact---
 ||||| |||||||| || | ||| || |||||||||||||| || || |||||  |  |||| |||||| |||| || |||||||||||||||| | |||| | |  |||   ||   | |||    | |||        ||| |||  | | |   ||||||||     | ||||        |||  |    | |     
AGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAACAACACTGATGGTTTGgtaaattatcttcattggatatcatctctcaagtaatcatcattgtatggatatt---aattttactatagattgttgtgagcacaattctaacgctagatta

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaa-gtgtttatgctgtaatgtttcttccact
 ||||||||||||||||| | ||| || |||||||| ||||| ||||| |||||  |  | || |||||| |||| ||||||||||||||||| | | |||| | | ||||    |   | |  |     |||| | || |  | ||||  |   ||| |      ||| |  ||| |     | || || | |    | |
AGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAACAACACTGACGGTTTGgtaaattctcttcacttgatattcccttacaagcagtatcatctttatt-gatactgagaaggagaatacatcgtgatacatttttattgatgccgatatt

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ24533 (Selaginella moellendorffii), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact
||| || ||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || |||| ||||||||| | || ||| ||||||||||| | |  | | | ||   |||      |  |    | | |  |  |      | |  |                                         
GGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAGCAGCACCGATGCTCTGgt-actgttttagatttccttttttgttttcaat--cgtgatctacaagacgtgctccag----------------------------------------

upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ08154 (Selaginella moellendorffii), 5'ss of exon 3
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgt----cattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact
||| || ||||||||||| |||||||| ||||||||||| ||||||||||||||||| || || || |||| ||||||||| | || ||| |||||||||||      |||   |   |||| | |      |   |    | ||    |  || |                                                
GGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAGCAGCACCGATGCTCTGgtactgttttagatttccttctttgttttcgattgtgatctacaagacgtgctccag-----------------------------------------------

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|211535182|gb|FL238609.1|FL238609
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|166467014|gb|EG122028.1|EG122028
EST:     GGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAG
genomic: GGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAG
EST: gi|21330796|gb|BQ486177.1|BQ486177
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|60399000|gb|DN231816.1|DN231816
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|211532193|gb|FL238605.1|FL238605
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|211532190|gb|FL238602.1|FL238602
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|211535183|gb|FL238610.1|FL238610
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGGAGAGCCAGGGC
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGG-AGAGCCAGGGC
EST: gi|76016402|gb|DT943572.1|DT943572
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
EST: gi|211532184|gb|FL238596.1|FL238596
EST:     AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGGAGAGCCA
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGG-AGAGCCA
EST: gi|32802499|gb|CD954735.1|CD954735
EST:     GGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTG                         ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG
genomic: AGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactc ... gaacttgcagATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAACAACACTGATGCTCTGgtcattactctcgtttctgtttcacaagtgaagcggcataaattctattcaaagttgaaattttacatagaagtgtttatgctgtaatgtttcttccact

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG