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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGATCTTAATCTTATCAAGGAATTGGGCTTAAAGCTCGTGTTTGCTATGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagttttgtgcttctaggaatgttttgatggatttttcttttcacagccacacactttgttatccttggtaatatgtttagctaatggtatgaacttgcag

Basic information

species Zea mays
transcript GRMZM5G816356_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816356_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g47690.2 (Oryza sativa), 5'ss of exon 2
CAGAGATCTTAATCTTATCAAGGAATTGGGCTTAAAGCTCGTGTTTGCTATGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagttt-------tgtgcttctaggaatgttttgatggatttttcttttcacagccac-acactttgttatccttggt---aatatgtttagctaatggtatgaacttgcag
 |||||||| |||||||||||||| |||||||| ||||| || | |||||||||||| ||||| ||||||||||| ||||||||||||||| ||||||| ||||  ||||        ||  ||||| |  || || ||||   |||| ||||||| || |   | |||||||| || |||||   || ||| | | || |||| ||| ||||||||
TAGAGATCTCAATCTTATCAAGGAGTTGGGCTTGAAGCTAGTCTATGCTATGAATACCCATGTGCATGCTGATCATGTCACTGGAACAGGATTAATAAAGgtaaatagttccaacctctgaacttctcgagatcttgtgatatgtttt-cttttcatagtcttgatactttgttctctttggtcataacatggtcatctgatggaatgtacttgcag

upper sequence: GRMZM5G816356_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G53580.1 (Arabidopsis thaliana), 5'ss of exon 2
CAGAGATCTTAATCTTATCAAGGAATTGGGCTTAAAGCTCGTGTTTGCTATGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagttttgtgcttctaggaatgttttgatggatttttcttttcac----agccacacactttgttatccttggtaatatgtttagctaatggtatgaacttgcag
 |||||  | || || ||  | || || ||  |||||||  | | ||||||||| |||||||| ||||||||||| |||||||| || |||||  | || ||  |   | |  |||||   |  || | || ||   |   |  |||       |  |  | | |  || |||  |  |  | || |   |  |                
TAGAGACTTGAAACTGATTGATGAGTTAGGACTAAAGCTTATCTATGCTATGAACACTCATGTTCATGCTGATCATGTCACTGGTACTGGACTTCTTAAGgtctgttttctcttgcttgatgttatttgtttatatttccatggttttggtttaaatcgaagattcagtgatctatctttgtttgctccacacag---------------

upper sequence: GRMZM5G816356_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv12s0028g00630.t01 (Vitis vinifera), 5'ss of exon 2
CAGAGATCTTAATCTTATCAAGGAATTGGGCTTAAAGCTCGTGTTTGCTATGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagttttgtgcttctaggaatgttttgatggatttttcttttcacagccacacactttgttatccttggtaata-tgtttagctaatggtatgaacttgcag---
 || || |||   ||| | || ||| | || || |||||| | | ||| |||||||||||||||||||||||||| || || ||||| || || ||||| ||      | |     |  |||   |||||   ||   ||||||    |  ||  ||   ||   || | ||   |||  |||||| ||  |  |      |||  |   
GAGGGACCTTTCCCTTGTGAAAGAACTAGGATTGAAGCTCATTTATGCAATGAATACTCATGTACATGCTGATCATGTTACCGGAACTGGGCTGATAAAGgtt-----tctaacattcttagttctgtttaactg---ttttctcagtattgctgcaggtttc--taacattttcaatgctgtttaactcttttttcagtattgttgcat

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|50337192|gb|CO532318.1|CO532318
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|93016907|gb|EB642427.1|EB642427
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|148945871|gb|EC891162.2|EC891162
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|76911212|gb|DV164201.1|DV164201
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|78077488|gb|DV505922.1|DV505922
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|211511961|gb|FL422084.1|FL422084
EST:     GAATACTCATTGTACGTGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGNGGAGCAAAA
genomic: GAATACTCAT-GTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|211112955|gb|FL390939.1|FL390939
EST:     TGAATACTCATGTACGTGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|50331455|gb|CO526581.1|CO526581
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|148930115|gb|EC872441.2|EC872441
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|78106798|gb|DV525216.1|DV525216
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|93283011|gb|EB675275.1|EB675275
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|71446302|gb|DR827352.1|DR827352
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|149098018|gb|EE183965.2|EE183965
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|148944080|gb|EC889165.2|EC889165
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|38687948|gb|CK144979.1|CK144979
EST:     TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAA                         ACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
EST: gi|21891626|gb|BQ744839.1|BQ744839
EST:     TGAATACTCATGTACATGCTGATCATGTCACTGGAACAGGACTAATAAAA                         ACTAAGCTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA
genomic: TGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagtt ... gaacttgcagACTAAGGTACCTGGAGTTAAGTCTGTTATTTCAAAAGCTAGTGGAGCAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGATCTTAATCTTATCAAGGAATTGGGCTTAAAGCTCGTGTTTGCTATGAATACTCATGTACATGCTGATCACGTCACTGGAACAGGACTAATAAAAgtaagaagttttgtgcttctaggaatgttttgatggatttttcttttcacagccacacactttgttatccttggtaatatgtttagctaatggtatgaacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT