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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgattcacctaatataatgtatgatgtgattctaacctcttggatcttgtgtatgtatcag

Basic information

species Zea mays
transcript GRMZM2G045330_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgc-----cttcatataatga---------ttca-----cctaat---ataatg-tatgatgtgattctaacc-tcttggatcttgtgtatgtatcag
|||||||| |||||||||||||||||||| || |||||||||| |||||| ||||||||||||||||| || ||||| || ||||| |||||||| |||||| || | ||| || ||| || |||| | | || || ||| | |||||| ||||| | | || || ||||||| | ||||
TTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATATGGTCAGCTGGATGCGTTCTTGCAGAGTTACTTCTTGGTCAGgttagtcactatatctttatctaaggaactgcaacattcaggttccttgattagattatgctgtgatgttattctgattatatttcataatgtgtatttgtcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgat-tcacctaatataat----gtatgatgtgattctaacctcttggatcttgt-gtatgtatcag---------------------------------------------------
||||||||| || || || ||||||||||| || ||||||||||||||||| || || ||||||||||| ||||| || |||||| | ||| | || |||||| || | || || | | | | || ||| || | | | | || || || || | || ||| | |
CTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTTCTTTTGGGCCAGgtttgtgtcattgatttgttttcattaattattattattactatgtactattatatgaatctactgcaaaatgaagtaaatgttctcttaattattttccacccatgtgttatctgaaataatttaaacttttgcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgattcacctaatataatgta--tgatgtgattct----aacctcttggatcttgtgtatgtatcag------------------------------
|||||| || || || || || |||||||| || |||||||| | |||||| || || ||||||||||| ||||| || |||||| ||||| | || |||||| | | || | | | | || || || | | | | ||| | || || | | || | || |
CTATCGGGCACCGGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGCCAGgtttatgtcattgcttttcttttattgttagaatggtgcaaatagtctcattttcaataattatttagttatttactgcctacatgctatctgacacacaaatggaatttttgaag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA13G30060.2 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt----------tgccttcatataatgattcacctaatataatgtatgatgtgattcta--acctcttggatcttgtgtatgtatcag----------------------------------------------
|||||| || || || || |||||||| || || ||||||||||||||||| || || ||||||||||| ||||| || ||||| | ||| | || |||||| || || ||||| | | | || ||| ||| || ||| |||| || || | ||| | | | |
CTATCGCGCTCCAGAACTTATATTTGGCGCCACAGAGTATACAAGTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAACTTCTTTTGGGCCAGgtttgtgtcattgatttgttttcatgaattattattattactatgtactattatatgaatctaccacaaaatgaagtaaatgt-tctcttaattattttccacccttgtgttatctgaaacaatttaaacttttgcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgattcacctaatataatgtatgat-gtgattctaacctcttggatcttgtgtatgtatcag-------------------------------
|||||| || || || || ||||||||||| || || || ||| ||| || || || |||||||||||||||||||| ||||| | ||||| ||||||||| | | ||| ||| | |||| | || | |||| | ||| ||| |||||| |
CTATCGGGCTCCAGAACTAATATTTGGTGCAACTGAATACACACCTTCTATTGATATCTGGTCAGCTGGTTGTGTTCTTGCTGAACTTCTTCTAGGACAGgtta--tactttctggcaatctatgcattaatgttgctcatacttaagattgttttgccttctttctgtgatatgtaatattgacttcccatagtttcaaatgtttgtttag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt----------tgccttcatataatgattcacctaatataatgtatgatgtgattctaacctcttggatcttgtgtatgtatcag-------------------------------------------------
|||||| || || || || |||||||| || || |||||||| ||||| || || || ||||||||||| |||||||| ||||| | ||| | || |||||| || || ||||| | | | ||| ||| | ||| | | | | | | | ||| |||| |
CTATCGAGCACCAGAACTTATATTTGGGGCCACAGAGTATACCAGTTCGATTGATATTTGGTCAGCTGGCTGTGTTCTTGCTGAACTTCTTTTGGGCCAGgtttgtgtcattgatttgttttcattaattattgttactacaatactatattgtataaattt--tccacgaaacaatgtaaatgttttcttgattatatgccacccatgtgttatctaaaacaatctaaactttttcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA04G06760.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatata-----atgattcacc--taatataatg-tatgatgtgattctaacctcttggatcttgtgtatgtatcag-------------------------------------------------
|||||| || || || ||||||||||| || || ||||||||||||||||| || || ||||||||||| ||||| || ||||| | ||| | || |||||| || | || || | || | | | || || ||| ||| || | | | | | || ||| ||||
CTATCGAGCACCAGAACTCATATTTGGGGCCACAGAGTATACAAGTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAACTTCTTTTGGGCCAGgtttgtgtcattgatgtgttttcattaattattgttactacaattctattatataaattt--tccacaaaatgatgtaaatgttctgttgattatctggcacccatgtgttatctaaaacaaattgaacttttgcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgattcacctaatataatgtatgat-gtgattctaacctcttggatcttgtgtatgtatcag-------------------------------
|||||| || || || || ||||||||||| || || || ||| ||| || || || |||||||||||||||||||| ||||| | ||||| ||||||||| | | | || || |||| | | || | |||| | || ||| | ||||| |
CTATCGGGCTCCAGAACTAATATTTGGTGCAACAGAATACACAGCTTCTATTGATATCTGGTCAGCTGGTTGTGTTCTTGCTGAACTTCTTCTAGGACAGgttataaatttctggaaatctatgcat-taatgttgttgatacttaagatttttttgctttctttctgggatatgttatattgacttcacgtagtttctaatgtttgtatag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 6
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt-----tgccttcatataatgattcacctaatataat--gtatgatgtgattctaacctcttggatcttgtgt-atgtatcag---------------------
||| || || || || || || |||||||| || |||||||| | |||||| || || ||||||||||| ||||| || |||||| ||||| | || |||||| | ||| || | | | ||| | | | ||| || | || | | | | | || ||| || | ||
CTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGCCAGgtttatgttattgcttttcttttgttattaaaatggtgtaaatagtctcatattaaataacaatttactgcctagtgccatctgacacacaaatggaatttttttaaag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA06G43620.2 (Glycine max), 5'ss of exon 6
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt-----tgccttcatataatgattcacctaatataat--gtatgatgtgattctaacctcttggatcttgtgt-atgtatcag---------------------
||| || || || || || || |||||||| || |||||||| | |||||| || || ||||||||||| ||||| || |||||| ||||| | || |||||| | ||| || | | | ||| | | | ||| || | || | | | | | || ||| || | ||
CTACCGGGCACCAGAACTTATGTTTGGTGCCACTGAGTATACTACTTCAATTGATATTTGGTCAGCTGGCTGTGTCCTTGCTGAGCTGCTTTTGGGTCAGgtttatgttattgcttttcttttgttattaaaatggtgtaaatagtctcatattaaataacaatttactgcctagtgccatctgacacacaaatggaatttttttaaag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 5'ss of exon 6
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt--tgccttcatataatgattcacctaatata---atgtatgatgtgattctaacctcttgg----atcttgtgtatgtat-cag
||| ||||| || ||||||||||||||||| || ||||| |||| ||| || || || ||||| |||||||||||||| |||||| | |||||||| ||||| | | |||| | | | ||| | ||||| | ||| || ||| || | ||| ||| |||
CTACCGTGCACCCGAGCTCATATTTGGTGCCACTGAGTACACAACTTCTATTGATATCTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTCTTCTTGGTCAGgtaaacaattctttcagtaaccagcttattcaatctccatgtgtatatttgcattaggactcattgtgactatatcatgttcttatgcag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggt-tgccttcatataatgattcacctaatataatgtatgatgtgattctaa--cctcttggatcttgtgtatgtatcag------------
|| || || || || ||||| |||||||| || ||||||||| || || || |||||||| |||||||||||||| || ||| | |||||||| |||||| || | || || || | | | | || | || || || || | ||| |||| |
TTACCGAGCTCCAGAACTCATCTTTGGTGCCACAGAGTATACATCATCCATTGATATATGGTCTGCTGGTTGTGTTCTGGCAGAGCTACTTCTTGGGCAGgttagtgtaaatttctaacctgttgagtatcttgagaactaaagcatctctccaaaatcttctgtaaacaatgtg-gtattatttatcttcacag

upper sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 7
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcata--------taatgattcacctaatat-aatgtatg---atgtgattctaacctcttg---gatcttgtgtatgtatcag--------------
||| || || ||||| ||||||||||| || || |||||||||| ||||| || |||||||||||||||||||| ||||||||| | ||||| || ||||| | || | | | | ||| | | ||| | || ||||| || || | | |||| || | |
CTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATATGGTCAGCTGGTTGTGTCCTAGCTGAGCTTCTTCTAGGCCAGgtgaacaatttgcacagcaattttcagttttgcactttctgccaatatctggaaatgtgttttagttctgtgataaaactttgttcatttgacttattttcggttacag

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|194716888|gb|FK934047.1|FK934047
EST:     TAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAG                         CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG
genomic: TAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgcc ... tatgtatcagCCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG
EST: gi|20508268|gb|BQ279947.1|BQ279947
EST:     TAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAG                         CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG
genomic: TAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgcc ... tatgtatcagCCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATCGTGCCCCTGAGCTCATATTTGGTGCGACGGAGTATACAAGTTCAATAGACATATGGTCAGCTGGTTGTGTTCTAGCTGAGTTGCTTCTTGGACAGgttggttgccttcatataatgattcacctaatataatgtatgatgtgattctaacctcttggatcttgtgtatgtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA