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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttgtgcacatatgctttagaacaatggacagaattcaggtgaatacagactcttttttgtg...

Basic information

species Glycine max
transcript GLYMA20G24830.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttgtgcacatatgct-ttagaacaatggacagaattcaggtgaatacagactcttttttgtg--
|| |  || |||||||| || || ||||| ||||| ||  |||||||||||||||| ||||| || || ||||  ||||||||||| |||| |   ||| | | |  || |  ||| |     |  || | ||  |   ||   | | | |   |     | |||  |     ||| |   |     
GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAAGATGGTTTCTTTAGTGTCAAGAGCAAAATGCTGgttagttgcccttcaca-catgcaatt--tttcagccaatactggaaattagtgattgttatattagtatgttgggaagtgcttctgtgctcctcaataaaaa

upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttgtgcacatatgctttagaacaatggacagaattcaggtgaatacagac-tcttttttgtg--
|| ||||| ||||||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||| ||||  ||||||||||| ||||   |  |  |  || |||      |   || ||||   | | |||  | || |   || |  |  |  || |  |     || || |     |   
GGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTGgttagttgtgtacctga--ttgtaatagacatctgttatttgcatata-atgtatcagtatggtgaaatgtttatagttttacttctacatcctaccaatttt

upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtc--atagcttataactacttttatttgtttgtgcacatatgctttagaacaatggacagaattcaggtg--aatacagactcttttttgtg
|| ||||| ||||||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||| ||||  ||||||||||| ||||   |  |  || | ||   ||  |  ||  |||  | |     |    | | |   |||    | | |||   |   |   |  |||  ||||    
GGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTGgttagttgtgtacctgattgttttagacatccgttggttgcatatagcatttcagtatggtgaaatattgatagttctacttgtacctcgtactgatttt----

upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G121200_T01 (Zea mays), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactact-tttatttgtttgtgcacatatgctttagaacaatggacag-aattcaggtgaatacagactcttttttgtg
|| ||||||||||||||||| || ||||  ||||||||  |||||||||| ||||| ||||| ||  | |||| | |||||||||| ||||  || || || ||  || |||   |||   | |       |    | |   ||   |||   || | ||| ||    ||||     || |     
GGGGCTATCATGGCTGTTGGAGCGTCAAGACCTACTGTAGTGGCTGATAAGGATGGTTTCTTTAGTATCAAGAGTGAAATGCTGgttagtttattctcgtatct-gtatctaaaatttgagtataccgaagctctggttactgactgatgtttagtatttctggcatttacatgtaattgtgaag-

upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagctta-taactacttttatttgtttgtgcacatatgctttagaacaatggacagaattcaggtgaatacagactcttttttgtg--------------------------------------
|||||||| ||||||||||| || |||||||| |||||  | |||||||| |||||||||||||| || || || | ||||||||| ||||  || |  |  |||| |||      | ||  |||||   |   |         | || |   | ||| |   |   || || || ||   | ||                                      
GGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTGgtaagtt--ttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatag-cttttggctatgctaacagtaacattgtcgctttgttgttatgttggcag

upper sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttg-tgcacatatgct-ttaga-acaatggacagaattcaggtgaatacagactcttttttgtg
|| ||||||||||| ||||| || ||||||||||||||| |  |||||||||||||||||||||| || || | |||||||||||||||||  ||    ||  ||    ||    | ||   ||   ||   |   ||| |||||    |     |  || ||  |     ||    |  |||    
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc---

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|207747462|gb|GD720223.1|GD720223
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAGTGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|208183505|gb|GD987411.1|GD987411
EST:     GAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: GAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|19053677|gb|BM732344.1|BM732344
EST:     TGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAAATAAA-TGCTG                         GTGAATGTAACAGCTGATCATCGAATTATT-ATGGGG
genomic: TGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAA-TAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGG
EST: gi|9985549|gb|BE659657.1|BE659657
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|6134907|gb|AW133300.1|AW133300
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|14011336|gb|BG726189.1|BG726189
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|31464480|gb|CD406508.1|CD406508
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|21257189|gb|BQ454077.1|BQ454077
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|18735643|gb|BM528886.1|BM528886
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|208054335|gb|GD854472.1|GD854472
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGG
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGG
EST: gi|31466163|gb|CD408191.1|CD408191
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttgtgcacatatgctttagaacaatggacagaattcaggtgaatacagactcttttttgtg

- - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG