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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag

Basic information

species Glycine max
transcript GLYMA14G40570.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 4
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
| |||||||||||| |||||||||||||| |||||||||||||| || |||||||| || ||||| |||||      |||  |        | |  || |  ||  |     || |  ||  |  ||||| | |    | |  |  ||| |   |                
GCAAATCCAGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAGGGTCATTGCAGACCAGGCGAGgtacttccagtgaa--------tgtgctaatgcaggaatctggtggt--ttcataggacaggattaacctgctccaattgttgtctag--------------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G370852_T03 (Zea mays), 5'ss of exon 5
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgt---ttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
|  ||||||||||| |||||||| |||||  |||| |||||||||||||| || ||  | ||||| |||||   ||||| |||||  || ||     |    | |  |     |      |  |||| |  || | |    |||  |  ||||||  |                
GCTAATCCAGACTACAAGGGTGTCTGCCACATTGCACTTGCTCAGGAAGGCCACTGCCGACCAGGCGAGgtaccttgctgagttttccatgtacaggtcacctgtgattgtaga------acatgttgggaagcactaatcttctccaattgctatctag--------------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 5
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgt------ttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
|  ||||| ||||| || ||||||||||||||||| ||||| || ||||||||||| ||||||||||||||       |  ||   |  | | | ||   ||| || |  |  |  || |   ||||||||||      ||  ||||    |    |  ||| ||| |||       
GCTAATCCTGACTACAAAGGTGTTTGCCATGTTGCACTTGCACAAGAAGGTCATTGCAGGCCAGGAGAGgtaaagatctctttcactggatatgattggctttcttgtgattgaatatgg---atttgtttga------ttatgttcgaaatgatgtgttttttctattatag----

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 5
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcatt-gttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
|| || ||||| ||||| ||||| ||||||||||||||||| || ||||||||||| ||||| ||||||||    ||   ||  ||| |  ||||||| | |  | ||   ||   || ||| | |  || ||   | |||   ||||| | | ||||||            
GTTAACCCAGATTATAAAGGTGTATGCCATGTTGCTCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAGgtgcatttctcttgccaaatcattttttaatctgttcaattttttaatcctttatatt-cacaatacttgttgaacctttac-actttctcacag--------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 5
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattat--agtgaagcattgttcatttgtttg-acagaagtttggttcctcctttgctaatttctctgttacctgcag
|  ||||| || || || ||||| ||||||||||| ||||| || ||||||||||| ||||| ||||||||    ||   ||  |||||  ||||| |  ||  | | || | || |  || | | |   || ||   | |||   || |   ||  |||||            
GCCAATCCGGATTACAAAGGTGTATGCCATGTTGCCCTTGCCCAAGAAGGTCATTGCAGGCCTGGAGAGgtacatttctcttgccaagtcctttttcaaaatctatttaaactttttatatctttatatgcacaacacttgttgaaccctatatacattctcacag--------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 5
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaa---caagtttttttttattata--gtgaagcattgttcatttgtttgacagaagt----ttggttcctcctttgctaatttctctgttacctgcag--------------------------------
|  |||||||| || ||||| ||||||||||| |||||||| ||||| || |||||| | || |||||||| |   |     ||      |||  | |  | |||   ||   ||||  |     |  |||||| | |       |  | |  | ||   | ||| |   ||    |||                                 
GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAGgtatttgttacggaagttttcgttactgtcgaatatgccgtagtgcataatgttgctcgttgacatatgcagccccgtctaccacatttacagtttttggatttttcgcaagttaaatacgatcgtggcttcaatgggcgtag

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ32611 (Selaginella moellendorffii), 5'ss of exon 4
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
|  ||||| ||||| |||||||||||||| |||||||||||||| |||||||| ||  | || || |||||  |  |  | |   | || || | ||      ||||   |  ||||| ||||| | |   ||                                      
GCGAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGgtgagtctgatatttgatgtcttgtattgc----gtgagagacggttcagttgtt-gtctctag--------------------------------------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ16666 (Selaginella moellendorffii), 5'ss of exon 4
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
| |||||| ||||| |||||||||||||| |||||||||||||| |||||||| ||  | || || |||||  |  |  | |   | || || | ||      ||||   || ||||| ||||| | |   ||                                      
GCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAAGAAGGTCACTGCCGTCCGGGCGAGgtgagtctgatctttgatgtcttgtattgc----gtgagagatggttcagttgtt-gtctctag--------------------------------------

upper sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ16664 (Selaginella moellendorffii), 5'ss of exon 2
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag
| |||||| ||||| |||||||||||||| ||||||||||||||||||||||| || || || || |||||  |  |  | |   | || || | ||      ||||   |  ||||| ||||| | |   ||                                      
GCAAATCCCGACTACAAGGGTGTTTGCCACGTTGCTCTTGCTCAGGAAGGTCACTGCAGTCCGGGCGAGgtgagtctgatctttgatgtcttgtattgc----gtgagagacggttcagttgtt-gtctctag--------------------------------------

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|23733371|gb|BU764882.1|BU764882
EST:     GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
EST: gi|208286670|gb|GE085244.1|GE085244
EST:     GTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
EST: gi|209702338|gb|BW656311.1|BW656311
EST:     GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
EST: gi|193333560|gb|FK299506.1|FK299506
EST:     GGTCATTGTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GGTCATTGTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
EST: gi|208333788|gb|GE131159.1|GE131159
EST:     GTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
EST: gi|7684899|gb|AW755547.1|AW755547
EST:     GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAG                         GTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA
genomic: GTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttag ... ttacctgcagGTTCTCTTAGGTACTGATTCTCACACTTGTACTGCTGGAGCATTTGGTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAATCCAGACTATAAGGGTGTTTGCCATGTTGCTCTTGCTCAGGAAGGTCATTGTAGGCCAGGAGAGgtttgcttagtttaacaagtttttttttattatagtgaagcattgttcatttgtttgacagaagtttggttcctcctttgctaatttctctgttacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA