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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaagagctaggttttatcttccatatatacaatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag

Basic information

species Zea mays
transcript GRMZM2G170400_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g47540.4 (Oryza sativa), 5'ss of exon 3
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaag--agctaggttttatcttccatatatacaatcggttggtcactaat-aaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
 |||||||| |||||||| || ||||| ||||||||||||||||||||||||||||||||||| |||||||| || || || |||||||| ||||| |||||  ||     | ||    |||  ||| | ||  |||| || ||   | |  | | |||   | ||   ||      |||||     |  |     | |  |     
TGGCCATATATTCTTTAGGGAGTCATGCTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAATCCAACACATTACCGGGAGCCAAGGTTCTATACAAAGgttacagcttcaactcaagttt--ctttcttaattacagtcagtc--ttaaaagtgaaattttgctaactctacaacttccaacctttgtttgccctatatatt---

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g47545.1 (Oryza sativa), 5'ss of exon 5
--------------------------------------------AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaagagctaggttttatcttccatatatacaatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
                                             |||||||| |||||||| || ||||| ||||||||||||||||||||||||||||||||||| |||||||| || || || |||||||| ||||                                                                                                             
GTCGAGAAGCTAGTAGGAAGAATGGTGAAATGGCTGAAGgtaggtggccatatattctttagggagtcatgctttcaccaatctggagattccaaaaggaaggtgaatccaacacattaccgggagccaaggttctata-------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G33790.2 (Glycine max), 5'ss of exon 4
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaagagctaggttttatcttccatat-ata-caatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
 ||  |||| |||||||||||||| ||||| ||||||||||||||||| || || ||    ||||| || |||||  | ||||| || ||||||||||||||          ||   | ||| | | || | | | || ||  || ||   |     |  ||    ||  ||     |    | |  |  | ||| | || |    
TGGATATATATTCTTTAGAGAATCTTGTTTCCACCAATCTGGAGATTCAAAGAGAAAATACAACCCTACTCACTACAGGGAACCCAGATTTTATACCAAGgt--ttgttctttaaagtgtatttacaatcttacatcactcccttagtttgtgccggaaaat-tgttagaataagaatgagctggacatcaatttagggctcc---

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G05330.1 (Glycine max), 5'ss of exon 2
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtac-----caaagagctaggttttatcttccatatatacaatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
 ||  |||| |||||||||||||| ||||| ||||||||||||||||| || || ||    ||||| || |||||  | ||||| || ||||| || |||||         ||    ||| |   ||||| |||  |  |  |  ||| ||  | |  |||   |      |     |   |      || |  ||   |||       
TGGATATATATTCTTTAGAGAATCTTGTTTCCACCAATCTGGAGATTCAAAGAGAAAATACAACCCTACTCACTACAGGGAACCCAGATTTTACACAAAGgtttgttctttaaagtgtagttacaatcttacat-cactcccttagtttgt-gccagaaaattgtttgagttggacatcaacttaggactca-gttggagtgt------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G30650.3 (Glycine max), 5'ss of exon 1
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgt-accaaagagc-taggttttatcttccatatatacaatc--ggttggt-cactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
 ||  || | ||||| |||||||||||||| |||||||||||||||||||| || ||    |||||||| |||||| | ||||| || ||||| || |||||       |||| ||  |  |||   |  | | |||  |         | ||  | ||||    | | |  ||     ||    | |  ||| ||||| |        
TGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAAAATACAACCCAACTCACTATAGGGAACCTAGATTTTACACTAAGgttggttccgagcgtaattactattccctctttgtacctttcaaacaaatgcatgactaaaaatgagtttgacagcaactttatatgg--aatgttttttta-------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G11580.1 (Glycine max), 5'ss of exon 4
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgt--accaaagagctaggttttatcttccatatatac-----aatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
 ||  || | ||||| |||||||||||||| |||||||||||||||||||| || ||    ||||| || |||||| | || || || ||||| || |||||            ||  |  |||   |  | | | |     || |  |||  ||  ||||||      |  |       |||  |     |  | |||            
TGGATATGTATTCTTCAGAGAATCATGTTTCCACCAATCTGGAGATTCCAAGAGAAAATACAACCCGACTCACTATAGGGAGCCTAGATTTTACACTAAGgtttgtttcgagtgtaattactattccctctttgtccctttcaaacaattg--catgaataaaatgaggttgacagcaactttatatggaatgctctttact---------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 5'ss of exon 5
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgt--accaaagagctaggttttatct-----tccatat-atacaatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag
|||   | | ||||||||||| || |||||||| ||||| || ||||  ||||||||   |||||| ||||||||||| ||||| || ||||| || |||||    |    |  | |     |||      || | || | |||||       ||   || | | | |||| ||| |||  || |   |   |   |||   |         
AGGTTTTCTCTTCTTTAGAGAGTCTTGTTTTCATCAATCAGGTGATTTTAAAAGGAAAAAGAACCCGACACACTATCGTGAACCCAGATTTTACACAAAGgttagtcttttattttgacaccatcacatagtcaacattacacaatgaaacactcgtaaaaagaacctactttat-atttcttcct--tgagttgcattgcag---------

upper sequence: GRMZM2G170400_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 5'ss of exon 4
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaagagctaggttttatcttccatatatacaatcggttggtcactaataaaccatactct----atcattgtt-ttccagtagctaatatttttgtgcacacag-----------------------------------------------------------------
 ||   | | ||| ||||||| || | |||||| ||||| || ||||   |||| ||    ||||| ||||||||||| |||||||| |||||||| |||||     |||  |   | |||   | ||| ||  | ||   || || | |  || || |||        |  ||| || ||  || |  |  ||  |    |||  ||                                                                  
TGGTTTTCTCTTCCTTAGAGAGTCTTCTTTTCATCAATCGGGTGATTTTCAAAGCAAAAACAACCCCACACACTATCGTGAACCAAGATTTTATACAAAGgtt----agactttcatctta--ctacatgtagtccatt--tttgtgattcctacactataacaagagaaagattattgtttaaggaatttgtacataaaagcatccatattgaagggcttaaatatgtaaatgtttttcttacttcatatttctattttgagttgtaatgcag

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|211037925|gb|FK976248.1|FK976248
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211517250|gb|FL335505.1|FL335505
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211422123|gb|FL330491.1|FL330491
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211037926|gb|FK976249.1|FK976249
EST:     AAASGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATC
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATC
EST: gi|211040366|gb|FK976250.1|FK976250
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211040368|gb|FK976252.1|FK976252
EST:     AAAGGAAGGTGAACCCAACACACCATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211148345|gb|FL363504.1|FL363504
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211298361|gb|FL367935.1|FL367935
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
EST: gi|211040371|gb|FK976255.1|FK976255
EST:     AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAG                         GTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT
genomic: AAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaaga ... gtgcacacagGTATTTAAAGAGGGCCATTCATTTGATCAAGATGGAGGTTCGTTTGAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCATATTTTCTTTAGAGAATCATGTTTTCACCAATCTGGAGATTCCAAAAGGAAGGTGAACCCAACACACTATCGAGAACCAAGGTTTTATACCAAGgtaccaaagagctaggttttatcttccatatatacaatcggttggtcactaataaaccatactctatcattgttttccagtagctaatatttttgtgcacacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA