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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg...

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg----
|| || || |||||||||||||| || ||||| || ||||||||||| ||||||||||||||||| ||||| ||| |||| || ||||| ||||||   ||  | |    ||  |  | | |   ||   |  |  |      | |  |  |  ||   |     |||    |    ||    | |  || |     
TCATCGGTTCTTCATTCACAACCAAAATCAACAGTTGGAACTCCAGCTTATATTGCTCCAGAAGTTTTGCTCAAGAAAGAATACGATGGAAAGgtat--tatctatcccctttgtgctttaaaagttg--ccatcctgcatgcaaagatacactgataccagcagctgcccaacttctatgccttttgctcgacaat

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtaga-gtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg-
|| || || |||||||| ||||| ||||||||||| ||||| || || |||||||| || |||||  || ||||  |||| |||||||||||||||   || |   ||   ||  |  ||||    | | ||| ||  | |  | ||      |  |    | || |||  |   |  ||||  ||||||  |  
TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAGgtacttgtgcgactttccttatttatcttgagatgtgtctttaagagttgtgtatacctctgcatca-gtgcactgtagttcca-taaacatgtgccgcgtg

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 5'ss of exon 7
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtaga-gtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg-
|| || || |||||||| || || ||||| ||||| ||||| || || |||||||| || ||||| ||| ||||  |||| |||||||||||||||   || || |    |||  ||   | |    | |    |   | |  |  |      |  |    | || ||| ||   |  || |  ||||||     
TCATCTGTTCTTCATTCCCAGCCGAAGTCCACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTTTGTTGAAAAAAGAATATGATGGCAAGgtacttgtgctatcactttttttatcttgagaaatgtgtcttgagagttgtgcatacctctgcatca-gtgcactgttgttcca-tatacatgtgccacatg

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg
||||| || |||||||||||||| ||||||||||| || ||||| ||||| || |||||||| ||| ||||    || || ||||||||||||||| ||   |||  ||      | || |      | ||||||||  ||| |      |||  |  || |  | | |   || | ||  |||         
TCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAGgtaaaggcttttagag-----aattcctctgtaatctctgtatt--tctaag-----gatgaatagccaatcattg---agtgttacggttaccag----

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtacttt--ttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgcc-ttgg----------------
||||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| |||||  |  | ||    || || |||||||||||||||  |   |      | || |   ||||     |    |    |||  | ||| | |   || |   | |    |  |  ||  ||    |        |||                
TCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAGgtaaggccatgagaccaattcctctgtctagagttcaaaccagcttatccatatgactgtttataccacaaatattctttgagttgtcctctgaaatagctggtgttacatttttccag

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactttttagtttcatagtcttactctttttctgtat---taatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg
||||| ||||||||||||||||| || |||||||| |||||||| ||||| |||||||||||||||||  ||| |||||| || |||||||||||| |  ||  |||| ||| | |   | | |    ||  |  |    | | || ||| ||        |  |     | |  | |  ||||| |||     | 
TCTTCGGTGCTTCATTCACAACCAAAATCAACTGTTGGAACTCCTGCATACATTGCTCCAGAAGTATTAATGAGGCAAGAATACGATGGCAAGgtaaa--accatttaattttacatcttaatttcaattaagcttgtgcatttttctaagttctatccatgaaactttagctttatcaataaagatgtagtaag-

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactt---------tttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtg-cagcggtaaagttgtgccttgg------------------------------
|| ||  || | || || ||||||||||| || |||||||| || || || ||||||||||| || |||  |||| ||||||| |||||||||||    |  |           ||||||  || |   |    |  | | |   |  | || | | ||  |  | |  || | ||| || |    ||   | | |   |  |                              
TCCTCTTTGTTGCACTCCCAACCTAAGTCGACCGTGGGAACCCCCGCTTACATTGCTCCAGAGGTCTTGTCGAAGAAAGAGTACGATGGCAAGgtgagttcgtcggacgataacttagttgtattggtatggagtagtcccggcgttgtattgttagtttttccaagtaga-cgctgttgtcgatagtgtcggtatcggtcagctgagaagacagaaatgctttgatatgcag

upper sequence: GLYMA01G39020.2 (Glycine max), 5'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 5'ss of exon 6
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtaga------gtac-----tttttagtttcatagtcttactctttttctgtatta-atcttataatttgatagagggcg--agccctggtgcagcggtaaagttgtgccttgg----------------------------------
|| ||  || | || || ||||| ||||| ||||||||||| || || || ||||||||||| ||  |||  ||| ||||||| ||||||||||||        | ||     |||||     || ||  ||    |||  ||  || |  ||||   | |  ||  || | |  ||   |     |     || |       | ||                                  
TCGTCTTTGTTGCACTCGCAACCGAAGTCGACTGTGGGAACACCTGCCTACATTGCTCCAGAGGTCCTGCAAAAGAAAGAGTACGATGGCAAGgtacgtggtttgcacaagggtttttgaccgca-aggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtgtttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcag

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|58015703|gb|CX702445.1|CX702445
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|7693434|gb|AW761526.1|AW761526
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|21888347|gb|BQ741560.1|BQ741560
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|11413312|gb|BF425323.1|BF425323
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
EST: gi|58015395|gb|CX702137.1|CX702137
EST:     CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG                         ATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA
genomic: CAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtact ... ttaatatcagATTGCAGATGTCTGGTCATGTGGAGTAACCTTGTTTGTGATGCTAGTGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAGgtagagtactttttagtttcatagtcttactctttttctgtattaatcttataatttgatagagggcgagccctggtgcagcggtaaagttgtgccttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA