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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag

Basic information

species Zea mays
transcript GRMZM2G145595_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g23610.2 (Oryza sativa), 5'ss of exon 13
----------------------------GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
                            |||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||| ||     |||||| | || |  | | | |||  ||  |  |  | |  |   || ||   |||     |    | |   | |                                                 
TTTGCTCAACGCTGTTTACATCCCCCAGGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat-tatttgtcattgt--tgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag-------------------------------------------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
|||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||||| ||     |||||| | || |  | | | |||  ||  |  |  | |  |   || ||   |||     |    | |   | |                                                 
GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat-tatttgtcattgt--tgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcag-------------------------------------------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacat--gtgcctatttgccct----tatgctatatagtatatacata-------aatgattctttgtg-tgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag------------------------
||||| || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| |||||  | || |||||       | | || ||  | |    ||   | | || | ||  | ||       ||| |   |  |   | || |||  |||||||     | | |  |   |    |    ||| |  | |  |             | | ||||                         
GACATAAAATTTGCAGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAGgtgagctaatccttaattttcttccaataacttttctattctaaccttattaagacaataacaataaggaataaagaattgaaacaaagaacattcaccttcagacttgcacacacacagctagtttattgtcgcaggcgccttaacacatgtgtcttatattactgaggcag

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
||||| || ||||| ||||||||||| ||||| ||||| || ||||| |||||||| |||||  | || ||||    || ||  ||      ||    |  | |   | |   ||    |  | |  |  || ||  ||||  |  |     |   || | || |                                          
GACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAGg----tgagctaatccttaatttacttccaaaaactttttctattctagccgtattaagacaataacaataaggagaaaagagttgaaacatag-----------------------------------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtaca-tgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
||||| ||  |||||||||||||||| |||||  ||||||||||| | || ||||| || || || ||||||||| | |      || | |  ||    | | || |  ||| | |   || |||   |    ||||  ||| |||    |||   || || |||   |                                       
GACATAAAACTTGCTGTTCATGCACATCCAACACTGTCTGAAGTTGTAGACGAACTGTTTAAAGCAGCCAAGgtaaaatacaagaatctacatttgcattctctaatcaatagacat-cgaatctcgatt---aaaaggcaagcaactcctgt---ctatatcaatttcag-------------------------------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
||||| || |||||||||||||| || ||||| ||||| ||||| |||||||||||||| ||  | || |||||| |              ||||   ||| || |    ||  |   ||||   ||||     | ||   |     ||  | | |  | | |||      | |||  |    |  ||| |                
GACATAAAATTTGCTGTTCATGCGCATCCAACCTTGTCAGAAGTGCTGGATGAACTCTTTAAATCAGCTAAGgtaaa--------------cttacaatatttactgctaac--agccgattgagtgtggctgcagta---atctccttgtttctccatgctaaatgtaaaagcaatgagaagccagactt----------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag
||||| |||||||||||||||||||| ||||| ||||| || || || || |||||||||||  |||| ||||||   |  | | ||| ||  |||         |           | |||| || |   ||| ||  ||   | ||| |            || | ||   || | || ||                        
GACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAGgta--agctcttctttccctctatagacccctctgatcgacctgttaattcattat---aaagatttaat--agattggaa----agggagaatatgttgtcatacatagc------------------------

upper sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 14
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 14
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgc-cctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag---------------------
||||||||||||||||||||||| || || || || ||||||||| |||| || || |||||||| || ||||||  | |  | |  |     ||     | ||| || |   | |||||  ||  |||   ||   |  |      ||  ||    | | |   |   |   |   |   ||| |     || | ||   | ||                        
GACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAGgtatttctttcgaactcaaagtagttggtgtagcattt---tgaatgaacctcagtg--gaattcaggattgtgcttcatgtgtttcttcttcatgggacgatttatcctgcttcatttttctgctttctaaagcttgttggtttgagggttggcag

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|211470347|gb|FL451278.1|FL451278
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6672118|gb|AW282293.1|AW282293
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|20512800|gb|BQ279999.1|BQ279999
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|13249875|gb|BG360780.1|BG360780
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093993|gb|FL455618.1|FL455618
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211470346|gb|FL451277.1|FL451277
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|16378429|gb|BI992442.1|BI992442
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6865111|gb|AW360461.1|AW360461
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|13249874|gb|BG360779.1|BG360779
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32830615|gb|CD970293.1|CD970293
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|26456706|gb|CA828289.1|CA828289
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|20512799|gb|BQ279998.1|BQ279998
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6563894|gb|AW231516.1|AW231516
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32830552|gb|CD970230.1|CD970230
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093994|gb|FL455619.1|FL455619
EST:     GTTGTTTGAAGATCTGGATGAACTTTTCAAGGCTGCCAAA                         GTTAACACAGCCGGTTTGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: GTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32831600|gb|CD971278.1|CD971278
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|37377273|gb|CF625226.1|CF625226
EST:     CACACCCAACGTTGTGTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093992|gb|FL455617.1|FL455617
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacag

- - - - - - - - - - - - - - - - - -  CTGAAG