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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttag

Basic information

species Zea mays
transcript GRMZM2G019358_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 5'ss of exon 14
TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtataggaagcacttcatcctgatattc-caattcacaatgtgctctttcttccccca--aaaatgattttaacatt--cttcaaacatcttag------------------
 |||||||| || ||||| || ||||||||  ||||||||||  |||| ||||||||||||||||| || ||||| ||||||||||| || || ||||||||||||| ||| |||| ||  |  |    |||  ||    | | |   |  ||||||| |||  | |   | |  | |||    |||| | |  ||                    
CCGGGAAAGTGGCATTCCATATACTATTGTGCGGCCATGTGCTCTAACAGAGGAACCAGCTGGAGCTGACCTCATATTTGACCAGGGAGATAATATCACAgtatgtagaggcagcatttgtttgttgccttcataagatgccacgccattcttcttcctccataagatcaaataaagcatcagtttcatataagtttcctgtattttttttttcag

upper sequence: GRMZM2G019358_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA05G29330.2 (Glycine max), 5'ss of exon 14
TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgta-tgtatagg-aagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaa--atgat---tttaacattcttcaaacatcttag----------------------------------------------------------------------------
| | ||||| || ||||| ||    || || ||||| ||||||||||||||||| || ||||| |||||||| || ||||| || || || || || || ||| |||  |   ||    |  || ||  | |  |  |||| | ||  ||   |   |  ||||    |||||   |||    ||||| |    | || |                                                                            
TAGAGAAAGTGGCATTCCCTATGTAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCGATCTTATTTTTGATCAAGGAGATAATATTACGgtactgtgaaaacaaaagatggatgct--tttctcggttca-agtgctcttactaaactaccaatctcatgatatatttccgcttcttgatttctttttggcaattcatggtaactatatagtagcatgcattttgctcatttttccaaatgccaatctaatacaaagcttaacag

upper sequence: GRMZM2G019358_T03 (Zea mays), 5'ss of exon 12
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 5'ss of exon 14
TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtat----gtataggaagcacttcatcc-tgatattccaatt-cacaatgtgctctttcttcccccaaaaatgattttaacattcttcaa-acatcttag----
 |||||||| ||  | || ||  | ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||||| || || ||||| || || ||||     |  | |  | | || | |  || | ||    || | ||| |  |  | | || |     ||    || |||     || || | |||  |     
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatcaaagtggaattttaacagtgctgttgttgttgcccaacggtccatatgttgct----aagcttttctaattcattttaatatatccaacataa

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|10450883|gb|BE924807.1|BE924807
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211357416|gb|FL471654.1|FL471654
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7304470|gb|AW600409.1|AW600409
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|71760712|gb|DR958649.1|DR958649
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|13125927|gb|BG316602.1|BG316602
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503640|gb|FL133352.1|FL133352
EST:     GGTACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGAACA-CATCACA                         GGGAAGAT-TCCAAGGGGAGGAGTTGCCCCGTATTTGGTGTAGCAGCTCTG
genomic: GGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGA-CAACATCACAgtatgtatag ... aacatcttagGGAAAGATATC-AAGGGAAGAAGTTGCCC-GTATTTG-TGTAGCAGCTCTG
EST: gi|13562283|gb|BG550503.1|BG550503
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|16377470|gb|BI991944.1|BI991944
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503639|gb|FL133351.1|FL133351
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211501308|gb|FL133349.1|FL133349
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAAGT-GCCCGTATTTGTGTAGCAGCTCTGGC
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAA-GTTGCCCGTATTTGTGTAGCAGCTCTGGC
EST: gi|60352340|gb|DN219313.1|DN219313
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211501307|gb|FL133348.1|FL133348
EST:     AGGAATCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|32934374|gb|CF039186.1|CF039186
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGCCAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|12968100|gb|BG265047.1|BG265047
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|16378431|gb|BI992443.1|BI992443
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|148936819|gb|EC880960.2|EC880960
EST:     AGGAACCAGCTGGAGCCGATTTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGTTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|7216720|gb|AW562842.1|AW562842
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|12967873|gb|BG264820.1|BG264820
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
EST: gi|211503638|gb|FL133350.1|FL133350
EST:     AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACA                         GGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA
genomic: AGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtatag ... aacatcttagGGAAAGATATCAAGGGAAGAAGTTGCCCGTATTTGTGTAGCAGCTCTGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtatgtataggaagcacttcatcctgatattccaattcacaatgtgctctttcttcccccaaaaatgattttaacattcttcaaacatcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA