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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt...

Basic information

species Zea mays
transcript GRMZM2G374779_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 7
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgact-aataattc--gatgatatggtgacaagtttgtgtagt-----
|||||||||||||| || || || || |||||||||||||| ||||||||||| |||||||||||||||| |||||||       | |||||||    ||  | |||| |  |||  | |||   | | |||||| |  |||  |     ||     |    |        
GTCAAGAATTTCATTTCACTCGGTGGCCCTCATGCTGGTACTGCTTCAGTGCCACTTTGTGGTgtaagttcatctcat-------tgtttccaagtgatacctagtttgt-gatgaaaagttaaaatttaataatccaagattgtgcatggatcttctcagatgacacata

upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0488g00020.t01 (Vitis vinifera), 5'ss of exon 6
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttcca-atcac-tatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt------
|| ||||| ||  ||||  ||| ||| |||||||||||||||||||| || ||||||||||| ||||||     |      |||| |||  || ||||   |||  |  || |||  |      |||  | |  ||| |   ||| ||| |   || | |  |        
GTTAAGAACTTTGTCTCATTAGCAGGACCTCATGCTGGTACCGCTTCTGTCCCTCTTTGTGGGgtaagt--gcttttgtgatcatcattatcatatcatgcatgatgaattctaaaactgc---ttggtttaagattgggaaataaggtta---gtctatccaaaaaaggg

upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv15s0021g01760.t01 (Vitis vinifera), 5'ss of exon 7
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattat-ttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt---
|| ||||||||||| || || |||||||||||||||||||| ||||| || || |||||||| |||||||  |||  | || | ||   ||    ||||| | ||  ||    || |  |  ||   ||  |  ||  |  | |     ||  || |  ||  |   
GTTAAGAATTTCATATCACTTGGAGGTCCTCATGCTGGTACAGCTTCCGTTCCACTTTGTGGAgtaagttcttct--ttagccttttcattatgttcactttatgtgttgcacatactttacttgtgctt-tgttttcacaaaactcc-actggtctaagttttgaa

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|71763069|gb|DR961006.1|DR961006
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|33092681|gb|CF052675.1|CF052675
EST:     ACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: ACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|71311445|gb|DR792068.1|DR792068
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|24764991|gb|CA400152.1|CA400152
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|32934679|gb|CF039491.1|CF039491
EST:     GGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: GGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|76925921|gb|DV170650.1|DV170650
EST:     AGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTA
genomic: AGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGA-TTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTA
EST: gi|60353563|gb|DN220536.1|DN220536
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|74241744|gb|DT649658.1|DT649658
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|20802390|gb|BQ293440.1|BQ293440
EST:     CTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: CTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt

- - - - - - - - - - - - - - -  ATGCTG