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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag

Basic information

species Zea mays
transcript GRMZM2G038791_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 5'ss of exon 4
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag
|||||| ||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| |||||||  | ||||| ||||| |   | |      ||| | |||           |  | ||||   ||| ||  || | |   |||| ||   ||||   | ||||||| || |||
GATTACAGAAGCTGGTGCGAACCGTGTCCTTGTATGTGATCTTCATTCCAGTCAAGCCATGGGATACTTTGACATCCCAGTAGATCATGTTTATGGTCAGgtat--gcactgatgcatgttgactga------taactgctt-----------gcatgtgatttcatttatgattataact-ttgtctttctttttgattctttgatctgtcaag

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G44530.2 (Arabidopsis thaliana), 5'ss of exon 4
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttag--tgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag--
||||||  |  |||||||  |||||||||||| |||||||||||| ||  | ||  | ||||| |||||||| || ||||| ||||| ||||||||||||||| |       ||   |  | |||||||      | |||| | ||  | |   |  || |  ||  | |   | |||||||   | | || |  || | || |   || | ||||   
GATTACACAGTCTGGTGCAGACCGTGTCCTTGCTTGTGATCTTCACTCCGGACAGTCTATGGGCTACTTTGATATTCCAGTCGATCATGTTTATGGCCAGgtaga------aaaaagtttttcttaaat-----gactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtct-tcttttccttgtgctttaatattcatgaacag

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 4
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttag--tgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag
 ||||| ||||| ||||| ||||| || |||| |||||||||||||||| | ||  | ||||| || ||||| || ||||| ||||| || ||||| |||||| ||    |||    | ||| |    || ||   |    | |    | |   || |  |  |||  ||| ||| | |||||  |      |   |||  |||             
CATTACAGAAGCGGGTGCAAACCGAGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCTATGGGTTATTTTGATATTCCAGTTGATCATGTGTATGGACAGgta-ataaggtgatagcttctagt--ggtcaatgtgtatgatcagatttcaaactgatgctattggggttcttccatgttatacat-cagcatgactttggtgt-------------

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S42_193V6.2 (Physcomitrella patens), 5'ss of exon 4
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag-----------
 || || || ||||| |||||  | || || | |||||||||||||||  | ||  |||||||||| ||||||||  | || |||||||||||||| |||||   |    |||  | |    | ||  | ||  || | | ||| |  |  ||   |   | |   |  | | || || |  | | |||  ||      || || |||   ||             
AATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGTCAATGGGATATTTTGACATTTCCGTTGATCACGTTTATGGTCAGgtgagta---tgattcttagctcgtacttttaccaagtgcattatgtatgggt-cgtgcaacgaggt--aactttattcttttcgctttgaatgacctttgattaatctcggagccttgtgtgcag

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|211126323|gb|FL371824.1|FL371824
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|76014853|gb|DT942023.1|DT942023
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|91052223|gb|EB162641.1|EB162641
EST:     TCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: TCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|148941796|gb|EC886762.2|EC886762
EST:     TCAAGCAATGGGATACTTTGACATCCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: TCAAGCAATGGGATACTTTGACATCCC-AGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|71429936|gb|DR810986.1|DR810986
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|60350838|gb|DN217811.1|DN217811
EST:     ACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: ACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|71429935|gb|DR810985.1|DR810985
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|76011084|gb|DT938254.1|DT938254
EST:     TCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: TCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|76914467|gb|DV165542.1|DV165542
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTAT
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTAT
EST: gi|94476090|gb|EB705048.1|EB705048
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCCTCGC-AGCAAGACAATATGT
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATC-TCGCCAGCAAGACAATATGT
EST: gi|78118884|gb|DV537268.1|DV537268
EST:     GTCAAGCAATGAGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|91052224|gb|EB162642.1|EB162642
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|60398185|gb|DN231001.1|DN231001
EST:     CAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: CAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|78120522|gb|DV538906.1|DV538906
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|211341635|gb|FL411914.1|FL411914
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|71771273|gb|DR969210.1|DR969210
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|149077159|gb|EE165820.2|EE165820
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGT
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGT
EST: gi|21088968|gb|BQ401281.1|BQ401281
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|148965187|gb|EE015993.2|EE015993
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|101391941|gb|EB817900.1|EB817900
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGAATATCTCGCCAGCAAGACAATATGTTCAGATGACTTT
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTT-
EST: gi|31354058|gb|CD438415.1|CD438415
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
EST: gi|148931525|gb|EC874574.2|EC874574
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCT
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCT
EST: gi|26457160|gb|CA828743.1|CA828743
EST:     GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAG                         CCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG
genomic: GTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtac ... atccgtgaagCCTGTTATTCTTGATTATCTCGCCAGCAAGACAATATGTTCAGATGACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTACCGAAGCTGGTGCCAACCGTGTCCTTGTTTGTGATCTTCATTCTAGTCAAGCAATGGGATACTTTGACATCCCAGTAGATCACGTTTATGGCCAGgtatatgtactgaagcatgctacttaaatctattaattcctttaagacttagtgtttatgatggtattcatccttcttataattgttttctatttttcctgtttgatccgtgaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA