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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA

Basic information

species Zea mays
transcript GRMZM2G113592_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113592_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 3'ss of exon 6
gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttga--tctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                                           ||  |||  |||||    ||| |||||    || ||       |||||| ||||| | |  |||||| ||| | |    || ||   || ||||||  | ||| ||||| || ||||| || || || || |||| |||||||||||||||||||||||| |||||| ||||||| || ||||||||||
-----------------------------------------------------------aaacaaacaaacaattgtaatgacaaccggcaacat-------tcttaagttcagtgcatatttctttttggaaagaccttaatgggtacatttgagctttttgcagGTACGGCTTGTGACCGACAAGGAAACAAATAAACCTAGAGGATATGCATTCATCGAGTATATGCACACCCGGGACATGAAAA

upper sequence: GRMZM2G113592_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G38120.1 (Glycine max), 3'ss of exon 6
gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcagg--ggaactttct-tattgaatattgtttcattactaaatttgatctt--tccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                                                   |||   |   | ||     ||    | ||   | ||   | ||  ||    ||| ||||| |  ||| || | |||| ||  |||||||  |  |  |  |||||||  | ||  |||| |||||||||| ||| || || || ||||| |||||||||||| |||| ||| ||||||||||| 
------------------------------------------------------------------tgaaatgagggagttttgtttat---tttattttctttgcagctgaagaccagaattttctgttctgactagtttttcttttttaaattttcttgtgatttagGTTCGATTAGTTGCTGACAAAGATACAAATAAGCCCAGGGGTTATGCTTTCATTGAGTATCTGCATACAAGAGACATGAAAG

upper sequence: GRMZM2G113592_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 6
gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                                                 |||| ||||||  ||       || |   |  | |  |    |  | |    |  ||| ||| |  |  || ||| |    |   ||||| |||| ||||| || ||  | || || ||||| || |||||||||||||| ||||| |||||||| ||| |||| ||||| || |||||| 
----------------------------------------------------------------taagatcaaacatcatctgtttcaatatgttttcttgattcagatatgaatctacttttattactttagtttatttaacctttttctttgagctttgcagGTCCGACTCATTACCGACAAAGAGACTAGTAAACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAG

upper sequence: GRMZM2G113592_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S42_265V6.1 (Physcomitrella patens), 3'ss of exon 6
gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                                       |   | ||      ||| | | | ||  |  | |  |||   |  |||  |||   ||  ||||        |||       ||  | | ||       |||||  ||||| || ||||||  ||| |||  | |||     ||  ||||||||||||| |||||||||  |||||| || ||||||||||
------------------------------------------------------ttcgcattt-----tacagagatacttgtagatgatgata---cgcatttgtaag--cattggaagcagagggttgggctgacttgaactccttctgcctatcttctcagGTCCGACTTGTACATGATAAAACTTCAAAGGCTCCCCGAGGATATGCATTTATTGAGTATCAGCACACTCGGGACATGAAAA

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|15313685|gb|BI478905.1|BI478905
EST:     TCTACATGTGCAAG                         GTTCGTCTTGTAACTGGAGAAAGATACAAGTAAACCTAGAGGATATGCATT
genomic: TCTACATGTGCAAGgttagcacgg ... atctttccagGTTCGTCTTGTAACT-GAGAAAGATACAAGTAAACCTAGAGGATATGCATT
EST: gi|16137392|gb|BI894257.1|BI894257
EST:     GAAGCTCTACATGTGCAAG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAATCCTAGAGGATATGCATTC
genomic: GAAGCTCTACATGTGCAAGgttagcacgg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|15323613|gb|BI478906.1|BI478906
EST:     CTACATGTGCAAG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTACATGTGCAAGgttagcacgg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|16137327|gb|BI894192.1|BI894192
EST:     TGGAAGCTCTACATGTGCAAG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAATACCTAGAGGATATGCATT
genomic: TGGAAGCTCTACATGTGCAAGgttagcacgg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAA-ACCTAGAGGATATGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                              tctttcc  CT-rich tract
               ttattgaatattgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcacggctgttttaggctttatgcctgtctgtcgtgcagcataaaatatgctaaaaattaaaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT