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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag

Basic information

species Glycine max
transcript GLYMA19G22530.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 7
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag
 || ||||| || || |||||||| || || |||||||| || |||||||  ||||| ||||||||||||||||||||||| ||||| || ||| | ||||||  |||      | | | || |||         ||| | ||| |  | |  | |    || | |  ||     | ||  ||  || | || |   | | | ||||
TTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTCCTGCCACTGAAGCCCAGgtaagttt-----ctaatgcgttgtt------gggctctt-acagttgtgacatgttgggttagcattaagggc-ctaagcatgattgttgtcatcctctaccacag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G158479_T02 (Zea mays), 5'ss of exon 6
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag
||| ||||| || || |||||||| || || || ||||| || |||||||||||||| |||||||| ||||| |||||||| ||||| || ||| | ||||||   | | | ||   |   || || | |||  | | |     | |   |    | || || |     || |  ||   |||    |  |                
CTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACACCTGCAACTGAAGCCCAGgtaaactaact-gtcatgt--tgattcctgtacttttga-attgtggggcaggactaaagtttg-----atcactca---tattccctcag----------------

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 6
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttg---ttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag
||| ||||||||||| ||||| || || ||||||||||| |||||||| |||||||  |||||||| ||||||||||||  ||| || |||||  | |||||   |||   |    || |    |     ||  ||   | ||| | |    ||          || |    || ||  ||| | || |||  | | |            
CTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCCCCGCCACAGAGGCACAGgttatttttcctccacttaaaatataagaacataaatctttatgccttatggtactgtcctttctcagtgtcatgatataaactttactttacggtgcag----------

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 5
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgt--acctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttc-----ggaaaaattatgcaaaatatatttttggttactttttgctacag-------
||| ||||||||||| |||||||| || || |||||||| |||||||| || ||||  ||||| |||||||||||||| || ||||| |||||| | |||||     ||  | || | | ||      |  | | | |  |  |  || || |  | ||| |||      |    ||||||  ||  | || ||||  ||  |||     |||        
CTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTCCTGCAACAGAAGCACAGgttagttttcctctgcttaagaaaataatttgcagaccata-aagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 6
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgta--cctttatttgttg-aggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag
||| |||||||| || ||||| || || |||||||||||||||||||| | |||||| ||  |||| |||||||||||||| ||||| |||||  |||||||     || || |  |  |   |    ||  ||     || | ||  | |||   | |    ||   |    ||| | ||| |   | | |       || || | |||
CTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGCCTGCAACAGAGGCTCAGgtgggttttcatctactctaattgcaacttgggtg--cttcttaactgtaattgcatct---ttttcaaggtgtta-gaaaattgagtgtcttccataattctggtgcag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 6
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 5'ss of exon 5
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctat--gaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag
||||||||||||||| ||||||||||| || |||||||| |||||||| |  ||||| |||||||| |||||||||||||||||||| |||||| | || ||| | |  |          ||| ||||| |  || | ||       |||   ||    |  |  ||||||| |         ||||| |    |     |||  ||||
CTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCCCTGCCACAGAAGCACAAgtaacatcct----------gtgctttcaatgtattttattttgcaaatttcatactgaaggtatggaaaaactg--------atattctcatcttaacgttggcacag

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|6951794|gb|AW423862.1|AW423862
EST:     TGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: TGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|21888018|gb|BQ741231.1|BQ741231
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|9984923|gb|BE659031.1|BE659031
EST:     TGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: TGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|21595027|gb|BQ610344.1|BQ610344
EST:     ATGATGGTGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|13479755|gb|BG509098.1|BG509098
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|17401890|gb|BM178672.1|BM178672
EST:     TTGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|192323087|gb|FK017373.1|FK017373
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATAT-GTATCATTCCTGA
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGA
EST: gi|151407875|gb|EV277690.1|EV277690
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|192306981|gb|FG999986.1|FG999986
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAATATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|14008807|gb|BG725411.1|BG725411
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
EST: gi|9203731|gb|BE329955.1|BE329955
EST:     ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAG                         ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG
genomic: ATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttat ... tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCCCTGCTACAGAATCTCAGgtacctttatttgttgaggagtggtttcagtaaatctcatgacattgattatctatgaacttcggaaaaattatgcaaaatatatttttggttactttttgctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG