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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac...

Basic information

species Glycine max
transcript GLYMA16G27220.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G170595_T01 (Zea mays), 5'ss of exon 4
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaa--taacattacctagagacagctttaaaatttattcttttttagtgaaaaaata-tagatcatattatacttgtcaaatgagaaacagatatcaac------------------------------------------------
 |||||||| || || || ||||| ||||| || |||||||| || |||||||||||||| || || ||| | || ||||| |||||||||||||| |||  | |  ||      ||| |        ||| | ||  |    ||||| |||     |  |  ||  ||    |    ||||||            |||                                                  
ATGTGTGCTTGAACCAGGCGACAAAATTGTTGATTGCCCTCCAACATTCACAATGTATGAGTTCGACGCTTCAGTCAATGGTGCACTTGTTATCAAGGgtgtgtagctagtccctccttgtattttgcttatatttcttgaacttttaatgattctttggttaattttagctcatcactcaaattgatttttctcttcactgtatgcgtcttcccagcatgatatttcattcaccattctattatgtag

upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv06s0004g02170.t01 (Vitis vinifera), 5'ss of exon 3
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagaga-cagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac
 ||||| |||||||||||||||||| ||||||||||||| || |  |||||||||||||||||||||||||| |||||||| ||||||||| |||||||| |   | |       |||    ||    ||  | | |  | || ||| |||||    | |  |  |   |  ||| |   |        |  | | |  
ATGTGTACTGGATCCTGGAGACAAGGTTGTGGACTGCCCGCCAATTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAGgtaaagtttatgccttttagctttcaataatattagtgacaccttattactgaaagc-cacatttattgacacccttttttgaatttttctactttttagt

upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0072g00940.t01 (Vitis vinifera), 5'ss of exon 5
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagct-ttaaaatttattcttttttagtgaaaaaatatagatcata-ttatacttgtcaaatgagaaacagatatcaac-
 ||||| ||||||||||| |||||||||||||| || || || || |||||||||||||||||||||||||| |||||||| ||||||||| |||||||| |   | ||| |  || |    |  | ||| ||||  |||| ||||   ||| |  | ||  | ||  |    ||| | |||   |        | |    
ATGTGTACTGGATCCTGGTGACAAGATTGTGGATTGTCCGCCAACTTTCACAATGTATGAATTTGATGCTGCTGTTAATGGGGCACTTGTTCTCAAAGgtaaagtttacactttcttgctttaaatattataattctttctatttt---gaagatttctactttatggtccctcttcttaaacatggtttcctaacctgtt

upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: EDP01242 (Chlamydomonas reinhardtii), 5'ss of exon 2
-----------------------------------------TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac
                                          ||||||||||| || || |||||||| ||||||||||| || |||||||| ||||  || |  ||  | ||||        |  |  |        ||      |  |  |  |  | |   ||         |   | |   | |||        | |  ||                                  
GTGGGCTGCGGCGCGGACGAGCTGATCGACCTGCTCATGCGCTGTGTGCTGGAGCCCGGTGACAAGATCGTGGACTGCCCGCCCACCTTCACCATgt--gagtgagacccggcgg--------gggcgggccgggggcggcggcggtggcggtggcgtgggtgggcgcgtgggcgtgggcatgggt-gtgggcgtgggtggggcag---------------------------------

upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ04411 (Selaginella moellendorffii), 5'ss of exon 4
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac
||||    ||||   ||| |||||||||||||| || ||||| || |||||||||||||  |||||||| || || || ||||||   || ||||||||||    |  |  | |    |     |||||   | | ||||||  ||   |     |||||                                      
TTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAGgtcttgtttgcgattc----aagtttctttag--tctgttctttgcta--aagcttctatag--------------------------------------

upper sequence: GLYMA16G27220.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ31551 (Selaginella moellendorffii), 5'ss of exon 4
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac
||||    ||||   ||| |||||||||||||| || ||||| || |||||||||||||  |||||||| || || || ||||||   || ||||||||||    |  |  | |    |     |||||   | | ||||||  ||   |     |||||                                      
TTGTACATTGGAAGTTGGTGACAAGATTGTGGATTGTCCTCCCACTTTCACAATGTATGCGTTTGATGCCGCTGTCAACGGAGCAAGCGTCATCAAAGgtcttgtttgcgattc----aagttcctttag--tctgttctttgcta--aagcttctatag--------------------------------------

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|193460633|gb|FK429194.1|FK429194
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|42723210|gb|CK769109.1|CK769109
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|254330364|gb|GR841629.1|GR841629
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|192322955|gb|FK016686.1|FK016686
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|209716352|gb|BW650751.1|BW650751
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|192325038|gb|FK016164.1|FK016164
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTTGCTGAAGTT
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATT-GCTGAAGTT
EST: gi|192325422|gb|FK018378.1|FK018378
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTTGAATGTTGAACAAATTGCTGAAGTTG
EST: gi|193431465|gb|FK396091.1|FK396091
EST:     CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAG                         TTCCAAGGAGGCCAGATTTCAGCTTAGAATGTTGAACAAATTGC
genomic: CACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataa ... taaactgcagTTCCAAGGAGGCCAGATTTCAGCTT-GAATGTTGAACAAATTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGTGCTGGATCCTGGAGACAAGATTGTGGACTGCCCTCCGACCTTCACAATGTATGAATTTGATGCTGCGGTTAATGGAGCACTTGTTATCAAAGgtcagaataacattacctagagacagctttaaaatttattcttttttagtgaaaaaatatagatcatattatacttgtcaaatgagaaacagatatcaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacaga