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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct...

Basic information

species Zea mays
transcript GRMZM2G081812_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g38790.1 (Oryza sativa), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct-----
||||||||||||||||||||||||| ||||||||||||||||||||||||   ||||||||||| ||||||||||||||||||||||||||||| |||||||  |  |  || |||| ||| || |||| | | |||||   |||||||||  | |  || |||  |     | |||| |    |  ||||   |          
AGGCCAAGCACTTCAAGTGCCACGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGTCCGTCACCAAgtacgtcc--cccccccccccactttcctccccatcccc---tcgatctgcatccggttcaatcccgtagcccggattcggccagctagatttttggatggcgta

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G34280.1 (Glycine max), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcga--tctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct
| |||||||||||||||||||| || ||||||||||||||||||||||||   ||||||||||| |||||||||||||| |||||||| ||||| || |||| | |||    |  ||  |   ||||||  |  ||   |  | |   | |  || |  |    | |      | | || | ||       | |     |  
AAGCCAAGCACTTCAAGTGCCATGTCTGCCACAAGAAGCTCTCCACCGCCGGCGGCATGGCCATCCACGTCCTCCAGGTTCACAAGGAATCCGTCACTAAgt-ataaccctatttccctcttttctccttattatcttgggttagggttttctgctttacattttgttttatcattaatcatattaaacgaaaaaaaaagt-

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G05390.2 (Glycine max), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctc----------ttccccgcctcg-atctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct---------------------------------------------------------------------
| ||||||||||| |||||||| || ||||||||||||||||| |||||    ||||||||||| ||||||||||||||||||||||| ||||| |||||||   | |    | ||| |       | |  |           ||  | |  |   || |  |  | | |     | | |  | | ||  ||     || |||  |    |                                                                     
AAGCCAAGCACTTTAAGTGCCATGTCTGCCACAAGAAGCTCTCTACCGCTGGCGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAATCCGTCACCAAgtataaccctatttccctcttttctccttatttagggtttgagttttctgttttacatttttgttttcttgttaatagggttaatcatcggaatattgaaatatatggaatgcaagggttaatcatccacgtccttttcacaacaaattgttgagattttccctttttattctttctcag

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv03s0017g02160.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatct-ggcgcgactgattagataggggagatagctctgct
|||||||||||||||||||||| || ||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| ||||  |||||| |     ||    |  ||   |||   | | |    |  ||| ||     | | |||     |  ||     ||     ||     |   | | ||   
AGGCCAAGCACTTCAAGTGCCATGTCTGCAACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATCCACGTCCTCCAGGTCCACAAGGAGACCGTCTCCAAgt-acttttgctcttctcccatttctttcgttttcattctactctattcatcctttccttttcttcagcaattttggaggaattctttatcaatccctagc

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0011g01240.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaac---agcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcg-actgattagataggggagatagctctgct
|||||||||||||||| ||||| || || |||||||||||||||||||||  |||||||| ||| |||||||||||||||||||| ||| ||||  ||||||     |   | |||  |  |  |||    |   | |        ||   ||  | ||    | |    |  | | |   | | |   || ||| |       
AGGCCAAGCACTTCAAATGCCATGTCTGTCACAAGAAGCTCTCCACCGCCGGTGGCATGGTCATCCACGTCCTCCAGGTCCACAAAGAGACCGTTTCCAAgtactctctcaaacctttcttcttcctaaattatacatatgtataccg-cttgttcttgtgatggttgaccttggaatttgtggttttcggggattgtgag---

upper sequence: GRMZM2G081812_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ16991 (Selaginella moellendorffii), 5'ss of exon 1
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct
|||||||||| ||||| ||||| || || ||||||||||||||||| |||   || ||||   | || ||  | |||||||||||||||||| | ||||||| || |     | | |   | || || |    |  |     |   |  ||  ||     |                                       
AGGCCAAGCATTTCAAATGCCATGTCTGTCACAAGAAGCTCTCCACTGCCGGAGGAATGGTTGTCCATGTTTTGCAGGTCCACAAGGAGTCCATCACCAAgtaaggat----ttctccttctctttcatatgttctctaaatttctttcgcttctttgcag---------------------------------------

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|31361671|gb|CD446028.1|CD446028
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|71325031|gb|DR799198.1|DR799198
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|74034907|gb|DT535397.1|DT535397
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGNGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATCTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|26457010|gb|CA828593.1|CA828593
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCAGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACAGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|211108805|gb|FL115292.1|FL115292
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|22818963|gb|BU499053.1|BU499053
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCAGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACAGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|211109705|gb|FL115302.1|FL115302
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|87155380|gb|DY400169.1|DY400169
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCAGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACAGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|29946767|gb|CB816315.1|CB816315
EST:     CACAAGGAGTCCG-GACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: CACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|32910104|gb|CF014916.1|CF014916
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|20507162|gb|BQ279513.1|BQ279513
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCAGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACAGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|211108807|gb|FL115294.1|FL115294
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG
EST: gi|211108808|gb|FL115295.1|FL115295
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAA                         GGTTCCTAATGCAAAGCCTGCATAGGGAGTCAACGGAGATAGAGATATTTS
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTG-ATAGGGAGTCAACGGAGATAGAGATATTTG
EST: gi|26559878|gb|CA832113.1|CA832113
EST:     TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCAGTGACCAA                         GGTTCCTAATGCAAAGCCTGATAGGGAGTCAACAGAGATAGAGATATTTGG
genomic: TCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacag ... tttactacagGGTTCCTAATGCAAAGCCTGATAGGGAGTCAACGGAGATAGAGATATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCAAGCACTTCAAGTGCCACGTATGCCACAAGAAGCTCTCCACCGCCTCTGGCATGGCCATACACGTCCTCCAGGTCCACAAGGAGTCCGTGACCAAgtgagaacagcctccccgccccctctcctgctcttccccgcctcgatctgcgcctgcctcgatctggcgcgactgattagataggggagatagctctgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG