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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt...

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgta----------gtctttagaaccagtatgcaaat-gttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt---------------------------------------------------------------------
|||||| ||||||||||| || ||||| || || || || ||||||||||| ||||| ||||| || || |||||| | || |||||||| || |||||||||             |||  |      || || |    | | |||| |        |  || |     ||  |   || ||   |||| | |  || ||| |   |  ||                                                                     
GTTTGCTGCTATGGGAGTGAATATGGAAACAGCCCAATTCTTCAAACGTGATTTTGAAGAGAACGGGTCAATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacatatagcagacttttgaagttctgattcataccaatttgttatgcatggaaactaattctgctagtgtatatgtgcttattttctgtatggttatatatgcatcatttttaacagaagttgacctgattgttaaaggtagaacatattttctaacaccaggctactctgtttacag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt-
|||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| |||||||| || |||||| | || |||||||| || |||||||||      || ||  ||       |   |    ||||   | || || |  ||    |     |   ||   |   | || ||| || |  ||| |  | 
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttgtgaatttgtaaccaac-attcatttatcattttatttcttctaagggcgccataatcaattctgcaatgttttacatgcatctt

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttatt-cccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt
|||||| ||||||||||| |||||||| || || || || ||||||||||| ||||| ||||| || || |||||  | || |||||||| || |||||||||      || ||   |       || ||     |     |    ||| ||  |  |  |  | ||  | |   ||||   |  |||||  |   || | 
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCATGGAACGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttatgaatttgtgatcaacattcatttaccattttatttctcccaagagtgccataatcggttctgcattgttttagatgcatatt-

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt
||| ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||||||||| |||||||||||  ||| |    |   || ||   | || |  |   || |  |  ||||     | |||    ||  || ||||     ||  |  |  | || ||     ||  
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatc--ttgaagcaaattt-----tagttccaatgtttttctgaag--gtttctcattctgttttccgcacag--

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctt-tagaaccagtatgcaaatgttcttttattcccat--------ttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt----------
 ||||||||||||||||| ||||||||||||||||||||||| |||||||| || ||||| ||||| || |||||||||||||| || |||||||| |||||| |  | |  ||  | |||     | ||  ||  |     |        ||||   || |  ||  | ||||   ||      ||||| |   ||    || |  |           
TTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAATGGAGAGAGTGACTCTATTCCTTAACCTGgtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattccc-----atttctttgttgtttacttgccttcctgatttccttct--ttgtaattttatctatgtagtt
 ||||||||||||||||||||||||||||| ||    || ||||||||||| || ||||| || || || |||||||||||||| ||||| || ||| |||||    | |     | | | ||  |  | ||| |  |       || ||||    ||    |||  |||||  ||     ||   | | |||   | |   |    
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta--tctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgt--ggttgtgttcctagttcagaactagctcttattccttttccctg---

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttct----tttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaatt------ttatctatgtagtt------------------------------------------------------------------------------------------
 || || ||||||||||| |||||||| |||||    || |||||||| || ||||| || ||||| || |||||||||||||| ||||| || ||| ||||| | |  |    |||| | |   | |  |    |||   | ||||| |   || | ||     |||| |    |   | || |||||       |  ||| | | |                                                                                            
TTTCGCCGCTATGGGAGTGAACATGGAAACTGCCACTTTCTTCAAACGCGATTTTGAAGAAAATGGATCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta-tgtacatcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcag

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt
 |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| ||||| |||||||| ||||| ||  | ||| | || ||||||   | | ||   |  |||| ||||   ||||| |||    || | |||   |||                                           
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgtacgttatggattgacaatgccaatgcgtttttactcctccatcgt-gtttcgtacag-----------------------------------------

upper sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 7
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt
 |||||||||||||| || ||||||||||||||||||||||||||| | || |||||||| ||||| |||||||| ||||| ||  | ||| | || ||||||   | | ||   |  |||| ||||   ||||| |||    || | | |   |||                                           
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgtacgttatggattgacaatgccaatgcgtttttactcctccatcgt-gcttcgtacag-----------------------------------------

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|18734533|gb|BM528238.1|BM528238
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|22931741|gb|BU548880.1|BU548880
EST:     ACTTTGAGGAGAATGGCTCGATGGNNAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTANNNTTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|14259630|gb|BG882538.1|BG882538
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|8285807|gb|BE023366.1|BE023366
EST:     ACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|208232106|gb|GE031831.1|GE031831
EST:     ACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACT
genomic: ACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACT
EST: gi|16279376|gb|BI943404.1|BI943404
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|193510698|gb|FK467196.1|FK467196
EST:     ACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACGATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
EST: gi|16283538|gb|BI945603.1|BI945603
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACCTCTT-GTATTGCTCTTAC
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCAC-TCCTCGTATTGCTCTTAC
EST: gi|208116661|gb|GD917183.1|GD917183
EST:     ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTG                         GCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT
genomic: ACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtcttta ... ttcattatagGCAAATGATCCTACAATTGAGCGTATCATCACTCCTCGTATTGCTCTTACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA