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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacatctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag

Basic information

species Glycine max
transcript GLYMA19G25870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 2
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagt------actta--ttagttattaaatga-catctatttttctatcttgaagatta-ttaatcaaatacttcatgatgactgattctttctatgttttttgatag-------------------------
||  |    ||||  || ||  | ||||| ||||| || ||||| |||||||| || ||||||||||| |||||||| ||  | ||  | ||||| ||||||  ||      |||||  |||  |  | ||| | ||  |    |  | |   ||  || | || ||       || | |||||   ||      ||    || |||||                          
CCAACAAGTGAGATGCTACCAAGGAATGAAGTGCTCGGTGGATATATCTTTGTTTGCAACAATGACACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgtgatccaacttaccttatcttctgaatcatcacttggcatattgttccgagaataaattcatgctgctatttacgatgatcaatatcaaata-accttctgatatataatcatatattgctgttctgcag

upper sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 2
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagt--------acttattagttattaaatgacatctatttt---tctatcttgaagattatta-atcaaatacttcatgatgactgattctttctatgttttttgatag-----------------
||  |    ||||  || ||  | ||||| || ||||| ||||||||||||||||| ||||| || || |||||||| ||  | ||  | ||||| ||||||  ||         | | ||||  || |||||| | || || |   | | | || || |  | || ||    |   |     ||  | ||||  |    || | |  | |                  
CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatcccgtcccttttagaaatcaaatgataactgttctggattttttttaaaaaaaaatatatagttttgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcag

upper sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacatctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag
|||||| ||||||| || ||  | ||||| || ||||| || ||||||||||| || |||||||| || |||||||| ||  |||||||||| || |||||| | | |  | ||    ||    |     | |||| ||    |  | | |   | | ||  ||||  |||    | ||  ||  |  |           
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctag-----tgttttactgatattcaaactgcaagtaaataactttttgact-ttcatcattgttcag-----------

upper sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacat-ctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag---
|||||| | ||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||| || ||||||||||| ||||| || || ||||||||| | || | |||  || ||   | | || ||  |  | || |||    | | |      || | |||| |     | |  ||   ||  |  | | |||    
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgt-aatagtgatt--ttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttca-ggcattttacactcattaactcatataatatgtg

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|57574688|gb|CX547663.1|CX547663
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|16345270|gb|BI970865.1|BI970865
EST:     AATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGNNNAATAACACCAGGGCTAC
genomic: AATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|298165387|gb|HO011436.1|HO011436
EST:     GTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: GTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|11275143|gb|BF325466.1|BF325466
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|254340597|gb|GR850899.1|GR850899
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|15286212|gb|BI470103.1|BI470103
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|10237029|gb|BE805917.1|BE805917
EST:     CTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: CTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|15663461|gb|BI700832.1|BI700832
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAT
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|7233125|gb|AW568475.1|AW568475
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|192334782|gb|FK025273.1|FK025273
EST:     TTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|254339779|gb|GR857904.1|GR857904
EST:     ATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: ATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|254335019|gb|GR844804.1|GR844804
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|8283592|gb|BE021151.1|BE021151
EST:     GTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: GTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|192304166|gb|FG993492.1|FG993492
EST:     TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|4289775|gb|AI437974.1|AI437974
EST:     TTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|7693250|gb|AW761345.1|AW761345
EST:     GAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: GAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
EST: gi|58019845|gb|CX706587.1|CX706587
EST:     TGTCTGTACCAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTG                         GTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC
genomic: TGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtactt ... tttttgatagGTTTGCCTCCAAGGTATCGAGATTCTGTTAGGGCAATAACACCAGGGCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacatctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT