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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacattgccacttacttttcatagtctagttttagactcattttttaggtttatttgggtatccacttgatttcacttaagtgattgttttctca...

Basic information

species Glycine max
transcript GLYMA04G39250.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 5'ss of exon 5
GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacattgccacttacttttcatagtctagttttagactcattttttaggtttatttgggtatccacttgatttcacttaagtgattgttttctca-------
| |  ||||||| || ||||||||| |  | || ||  | || ||||| |||||||||||||||||||| || ||||||| ||    ||  |   |  |||| | | |  |   || ||    |    |   ||   ||||||    | |   |||   ||  | |     ||  |||       
GAACCGAGCTGGTGGGTACACCAGACTATTGCGAACTAGGATACGAGTTGGTGATGCTGCACCGATGGCATACATTGAgtaagc---ttctcttatgatttttaaaatggaaaatt-gatcagtgacct---ttccattgggttattagtcagttttttttttgcggggaattagtcagttttgt

upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G64650.1 (Arabidopsis thaliana), 5'ss of exon 5
GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacattgccacttacttttcatagtctagttttagactcattttttaggttt-atttgggtatccacttgatttcacttaagtgattgttttctca-----
 ||||||||||| |||||||| ||| ||||||| || || ||||| || ||||||||||| || ||||||||||| |||| |        | | || |||||| |  |    ||| | |      | ||   ||  | ||  || |   |    || ||   || ||  || |     |     
AGATAGAGCTGGTGGATACACAAGAATGCTTCGTACTCGCATTCGTGTTGGTGATGCTGCCCCAATGGCCTATATCGAgtaaa------acaagtttcttttctttattctttttaacagaagcatattgaattcgagtttagtttagtcacagttacaacaaaatggatgatgctatatttta

upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 5'ss of exon 5
GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacattgccacttacttttca--tagtctagttttagactcat-tttttaggtttatttgggtatccacttgatttcacttaagtgattgttttctca--------------------------------
 ||||||||||| |||||||| ||| |||| || || || || ||||| ||||||||||| || ||||||||||| |||| |    | |  |  ||  || |||     ||| |||||| | |||| | |  | |||   |    ||   | |     | | ||    | ||  |     |                                
AGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGAgtaaaactagtttcttttctttatcagtctttctggttttacattcatatctccatgttagatcaaataagaagtgttaatgatttggaagctttctggtgaactaatttggtcgatacttgatactttggatag

upper sequence: GLYMA04G39250.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 5'ss of exon 5
GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat-tgccacttacttttcatagtctagttttagactcattttttaggtttatttgggtatccacttgatttcacttaagtgattgttttctca-
 ||||||||||| ||||| || ||||| ||||| || || || ||||| |||||||||||||| |||||||||||||||| ||    | |   ||||  | ||   | | |  |||  || |||    |  |  | |     || ||      ||   | || ||    ||||     | 
AGATAGAGCTGGTGGATATACAAGATTACTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgtatttgacttgttattgcgattgttttttaggagtcaagcatctgtctgacactagtgtctttcgaatg--attttagaagatgttacaatat

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|26268298|gb|CA819361.1|CA819361
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|298187006|gb|HO034155.1|HO034155
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCT
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|192311623|gb|FK003106.1|FK003106
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|192310244|gb|FK002600.1|FK002600
EST:     CTTCGGACCCGTATTCGACTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|192310245|gb|FK002601.1|FK002601
EST:     CTTCGGACCCGTATTCGACTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|192311622|gb|FK003105.1|FK003105
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|31470250|gb|CD412218.1|CD412218
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|20814760|gb|BQ299238.1|BQ299238
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCT
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|7587908|gb|AW703714.1|AW703714
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|298174461|gb|HO014606.1|HO014606
EST:     CTTAGGATCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCT
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|23064422|gb|BU579195.1|BU579195
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|298189819|gb|HO038222.1|HO038222
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCT
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|14009072|gb|BG725667.1|BG725667
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|193592761|gb|FK546133.1|FK546133
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|16343728|gb|BI969323.1|BI969323
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA
EST: gi|105633466|gb|DW246829.1|DW246829
EST:     CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGA                         GTTTATTGACAGAGAAAATGAGCTTAGGCGGGCAAAGGCACCAACTCCTCA
genomic: CTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacat ... tttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGAGCTGGAGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATTGAgtgagtacattgccacttacttttcatagtctagttttagactcattttttaggtttatttgggtatccacttgatttcacttaagtgattgttttctca

- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC