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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct...

Basic information

species Zea mays
transcript GRMZM2G135283_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctcca-actatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct
 || |||||||||||||| |||||||| || ||||| |||||||| || ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||| ||      | |||||  |||| |  |  ||| |    |||  |||||||  ||| |||||||  ||||| ||||||||    || 
ACCTGCCAACTTCCATGTTTACACTGCCCTATTGAAACCACATGAGAGAATCATGGCTTTGGATCTTCCTCATGGTGGACATCTTTCTCACGGCTACCAGgtacatgggtctggacttcttcattgcctccttactactagttgtttcagttggcatgcaagcata-atgcttccttccttgttgtctttctttgtcctca

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgg--gtctggagtttccttgtacctccaac--tatttttattttgatgctgca-cacaagcatggatgtttccttctctgttgcctttctttcctttct
 || || || ||||| || ||||||||| |  | || || |||||||| ||||||||  | ||||||||||| ||||| ||||||||||| || || ||||||| | |  || || | || | |  | | |   |   |||  | |  |  |  ||| |        |||| | |||  |  | | ||| |||| | |  |    
TCCTGCAAATTTCCACGTTTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaagtttgaacttccatcattcatttcatcttataatgaaatgaaatctgtagtgtgtatatggctatttaataat-tattgtctttttatttt----

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA18G27710.1 (Glycine max), 5'ss of exon 7
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacat---gggtctggagtttccttgtacctccaac--tatttttattttgatgctgcacacaagcatg---gatgtttcct-tctctgttgcctttctttcctttct-----------------------------------------------------------------------
 || || || |||||||| ||||||||| |  | || || |||||||| ||||||||  | ||||||||||| ||||| |||||||||||||| || ||||||| |     || || | || |    | | |   |   |||  | |  |  ||  ||   | | |  |     ||  ||  | ||| | ||   ||  | || ||||                                                                        
TCCTGCAAATTTCCATGTCTACACTGCATTGCTTAAACCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCATGGATATCAGgtacttttgaagtttgaacttccaccattcatttcatcttataatcaaatctatagtgtgtatatggctatttaataattattgtcttttttattttgatatcttttcaaagattgagtagaccttggggtcattaatgaaaaattatactcgtttaatattgctgctataactacgcag

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgt-acctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct
 || |||||||||||||| ||||||||| | || ||||| |||||||| ||||||||  | ||||||||||| ||||| ||||||||||||||||| ||||| | |     |  | |||   ||| |  ||  |    | | | | |||||        ||  |  | |  || ||||| | || |   ||          
TCCTGCCAACTTCCATGTGTACACTGCATTGTTAAAGCCTCATGAAAGAATCATGGCACTTGATCTTCCTCATGGTGGTCATCTTTCTCATGGTTATCAGgtgccttcaagttaactttgtatgtcatttcggaactctctgactctgatg--------aataacagtttctttcttct-tatttctcatcag--------

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactattttt--attttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct--------------
 || || || ||||| || ||||||||| | |||||||| |||||||| ||||||||  | ||| | ||||| ||||||||||||||||||||||| ||||||| |||||       |  || |      ||   | | ||  | |||  |    ||        ||||  |    || | | ||  | |  |||| ||| |              
ACCAGCTAATTTCCAAGTTTACACTGCATTGTTGAAGCCTCATGAAAGAATCATGGCACTTGATTTACCTCATGGTGGACATCTTTCTCATGGTTATCAGgtacttgggttctagtctctctagcttggtcagtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctcttgtgcag

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct--------
||| || || || || || ||||||||||| || ||  | |||||||| || |||||  | ||||||||||| |||||||||||||||||||| || ||||| | |  | ||    |   || |     ||  |||  | ||      ||||   ||    | |    ||  |  ||| | ||| |||  |  || |           
GCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAAGCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGGTGGACATCTTTCTCATGGCTATCAGgtgcttatgact---ttcatctagagttccctgctagatatacc--agtgctttccat---cttctcagtggctgtctattttgacttattagccatgggaaaaaaat

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct--------
||| || || || || || ||||||||||| || || || |||||||| || |||||  | ||||||||||| |||||||||||||||||||| || ||||| | |  | ||    |   || |     ||  |||  | |||   | ||||   ||    | |    ||  |  ||| | ||| |||  |  || |           
GCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGGTGGACATCTTTCTCATGGCTATCAGgtgcttatgact---ttcatctagagttccctgctagatatatc--ggtgctttccat---cttctcagtggctgtctattttgacttattagccatgggaaaaaaat

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct--------
||| || || || || || ||||||||||| || ||  | |||||||| || |||||  | ||||||||||| |||||||||||||||||||| || ||||| | |  | ||    |   || |     ||  |||  | ||      ||||   ||    | |    ||  |  ||| | ||| |||| |  || |           
GCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAAGCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGGTGGACATCTTTCTCATGGCTATCAGgtgcttatgact---ttcatctagagttccctgctagatatacc--agtgctttccat---cttctcagtggctgtctattttgactttttagccatgggaaaaaaat

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct--------
||| || || || || || ||||||||||| || || || |||||||| || |||||  | ||||||||||| |||||||||||||||||||| || ||||| | |  | ||    |   || |     ||  |||  | |||   | ||||   ||    | |    ||  |  ||| | ||| |||  |  || |           
GCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGGTGGACATCTTTCTCATGGCTATCAGgtgcttatgact---ttcatctagagttccctgctagatatatc--ggtgctttccat---cttctcagtggctgtctattttgacttcttagccatgggaaaaaaat

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct---
 || |||||||| || |  ||||| ||| | || || || ||||| || ||||||||  | ||||||||||| ||||| |||||||| |||||||| ||||| | |  |  |    |    |   || |    ||      | ||  |    |    |     | | || ||    |   |     |||  ||   |||    
CCCTGCCAACTTTCAAGCTTACACGGCATTATTAAAACCTCATGAGAGAATCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatgagttccttcaattaagacttttgcctgccaa-acttgaacatggtgtcctgctcttggtgatta--accaagacaaattttattggattcaatt

upper sequence: GRMZM2G135283_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 5'ss of exon 6
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattt-tgatgct-gcacaca---agcat----ggatgttt-ccttctctgttgcctttctttcc-tttct-----------------------------------------------
||| || ||||| || || ||||| || ||| |||||||||||||  |||||||||| |||||||||||||| ||||| ||  | |||||||| || ||||||| |   |||||  ||   ||    | | |  |||  ||  || || |  | || || |   |  ||     |||| || || |   |  | | | |||   | |||||                                               
GCCAGCAAACTTTCAGGTGTACACAGCTCTCCTGAAGCCACATGAGCGGATCATGGCGTTGGATCTTCCTCATGGTGGCCACTTGTCTCATGGATATCAGgtacgtct-tctggttttctattcatgcccaatttatacttgcttgtggtatttgctcaaactgaatatcctaagatggttgccattcttactacgtatctgcacgtttctccacaatcatgaatttattcacacttcatgcttttcatggcaaacag

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|67019160|gb|CO447909.1|CO447909
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT
EST: gi|21987802|gb|BQ779330.1|BQ779330
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA
EST: gi|211286148|gb|FL173729.1|FL173729
EST:     TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAG                         ACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACA-TGCCT
genomic: TCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggt ... ctgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCGCCAACTTCCATGTATACACTGCACTCTTGAAGCCACATGAAAGGATCATGGCTTTGGATCTTCCTCACGGTGGACATCTTTCTCATGGTTACCAGgtacatgggtctggagtttccttgtacctccaactatttttattttgatgctgcacacaagcatggatgtttccttctctgttgcctttctttcctttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccaac