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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttgtgatttttaacttatgatgttatatctttcatattttcaagtgtttttaaactcttgatctcatattttgctttagccttttaatattga...

Basic information

species Glycine max
transcript GLYMA20G22600.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 9
CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttgtgatttttaacttatgatgttatatctttcatattttcaagtgtttttaaactcttgatctcatattttgctttagccttttaatattga---
|||||||| ||||| ||||||||||| ||||| ||||||||||| ||||||||||      ||  ||| |    || |||  | || |  |    || ||  |    |||||  | |  | || |   | |  ||| |   |  |  | |    
CCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAGgtaactacattgtatttcagtacatcatgcaaaatatagctcgattgca--ttaaattaaatacatcttttc-tgagtggaattaccggatctaggtgggagg

upper sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttgtgatttttaacttatgatgttatatcttt-catattttcaagtgtttttaaactcttg---atctcatattttgctttagccttttaatat-tga----------------------
||||||||||| || ||||||||||| |||||| | || ||||| |||||||||        |   |  |     |  ||||  |   |  | || || |  |    ||   ||| |||      |  |||  |||| | |  | | | ||| | |                      
CCTCTGTTCCCCGGAGAGAGTGGAGTGGATCAATTGGTGGAGATTATCAAGgtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcag

upper sequence: GLYMA20G22600.3 (Glycine max), 5'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttgt------gatttttaacttatgatgttata-tctttcatattt---tcaagtgtttttaaactcttgatctcatattttgctttagccttttaa-tattga---------------------------------------------------------------------------------
||| |||||||||| || || |||||||||||| | || |||||||||||||||   | |        || |   | | ||||  | |  | || ||  || |    |    ||| | |  | |     | |  |||| |  || |   | |||  |  |                                                                                   
CCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAGgtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacag

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|6566240|gb|AW233921.1|AW233921
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAT                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|22522569|gb|BU081380.1|BU081380
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|120495461|gb|EH223628.1|EH223628
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|12773850|gb|BG238777.1|BG238777
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|15287684|gb|BI471575.1|BI471575
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|14990268|gb|BI315941.1|BI315941
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|27426708|gb|CA938228.1|CA938228
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|11413300|gb|BF425311.1|BF425311
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGNTGAGATCATCAAG                         GNTCTGGGCACTCCAACAAAGGAAGAGATTAAGTGCATGAACCTTA-TTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|9258249|gb|BE346396.1|BE346396
EST:     AGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: AGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|209699788|gb|BW655801.1|BW655801
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|15000029|gb|BI320843.1|BI320843
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|254333710|gb|GR848628.1|GR848628
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|192321549|gb|FK012899.1|FK012899
EST:     CTCTGTTCCCTGATGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|6725763|gb|AW310162.1|AW310162
EST:     AGTGGAGTTGATCACCTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATAAAGTGCATGAACCNTAATTAT
genomic: AGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|14990090|gb|BI315763.1|BI315763
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|11412139|gb|BF424159.1|BF424159
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|192321548|gb|FK012898.1|FK012898
EST:     CTCTGTTCCCTGATGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|120492579|gb|EH220746.1|EH220746
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|13481205|gb|BG510548.1|BG510548
EST:     CTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|22525150|gb|BU083970.1|BU083970
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|13481244|gb|BG510587.1|BG510587
EST:     CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttg ... gtgctgacagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATCATCAAGgtaatctttgtgatttttaacttatgatgttatatctttcatattttcaagtgtttttaaactcttgatctcatattttgctttagccttttaatattga

- - - - - - - - - AGTGGA
- - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - AGATCA