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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt...

Basic information

species Glycine max
transcript GLYMA07G36040.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g22520.1 (Oryza sativa), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgt-----tcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt
||| || || |||||||||||||| || || ||||| |||||||| ||  | ||||| |||||||| || |||||||||||||| |||||||| ||||||||       |   |  ||   ||    | |||   || ||||||   | ||  |    |||   | ||   |   ||    || | | |   || ||   |    
GGCGATCAAGGCGGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACCCTCGGCGGGACATGCCTCAACGTCGGCTGCATCCCCTCCAAGgtgaccacgacgatgctctccccctcgtccctccccctctttttcgatctcctctctactgtcttgcgggttcggttg---aggtggatgcgattttagatct--

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g06750.1 (Oryza sativa), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgt-tcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt----
 ||||| || ||||||||||| || || || ||||| |||||||| ||  | || || ||||| || ||||||||||||||||| |||||||| |||||||| ||     || |   ||||     ||   | ||    | ||    ||  || ||| |  |       |   |  ||| ||    | | || ||          
CGCCATCAAGGCGGCGCAGCTAGGGCTCAAGACCACCTGCATCGAGAAGAGGGGAACGCTCGGGGGCACCTGCCTCAACGTCGGCTGCATCCCCTCCAAGgtatcgccccctccctcccgccccgtctccgcgccgcgatctggga-tggatggctgcgcgtt----ccccgctgttagctctcggagagctcgtagatccgtgc

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G462140_T01 (Zea mays), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcatt-ttctagttcgtttaaatcttgtgttgtt---
||| || || || ||||||||||| || || ||||| |||||||| ||  | |||||||||||||| |||||||||||||||||||||||||| ||||||||     | |   |   ||  ||  |   | | |  | |  ||  |  | |  ||| |   | ||  || || ||    |  | | |  | |  | | |     
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACTCTCGGCGGGACCTGCCTCAACGTCGGATGCATCCCATCCAAGgtga---tgccctagctcgtcttctcagcttctcgctctg-gtaaccccattgctgtgccaccaatctctttgttgcgatgtgatgatgtttgatctggggtat

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G335657_T01 (Zea mays), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt--------
||| || || || ||||||||||| || || ||||| |||||||| ||  | ||||| |||||||| ||||| ||||||||||||||||| || ||||||||     | |   |   |||  |  |  | | |||       || |||     |    ||       |   || |||  |  | ||   |||  | ||||        
GGCGATCAAGGCCGCGCAGCTGGGGCTCAAGACCACCTGCATCGAGAAGAGGGGCACCCTCGGCGGGACCTGTCTCAACGTCGGATGCATTCCATCCAAGgtga---tgccctagctcgccgtctccct-ctcctgcccccattgctgtactacaccaatct----ctttgttgctacgtgatgtatgactttgggtgttagatctgt

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G48030.1 (Arabidopsis thaliana), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaa---attcattttctag----ttcgtttaaatcttg--tgttgtt-------------------------------------------------------------------------------
 || || |||||  | ||||| ||||| ||||||||||| ||||| ||||| ||| ||||||| ||||| || ||||||||||| ||||| |||||||||||  | ||||   || |  || |   || | |  |   ||||||  |    ||    ||||   |    ||| |||| | |    ||| ||| |   ||   |  |||                                                                                
CGCGATCAAAGCCTCTCAGCTTGGTCTCAAAACCACTTGTATCGAGAAACGCGGCGCTCTCGGTGGTACTTGTCTCAACGTCGGTTGCATTCCTTCCAAGgtcaaatttc--gaatcatctctcgtttcttcaatcaatttgttgatcatagttgacgattttgatctgttccttttgtggatgattcttttgagagttaattactgtcttttgtgatgattatcatttgcttaagcacagttattccataattactaaattcttggttgtgtttattgatgtattag

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G17240.3 (Arabidopsis thaliana), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttg--tgttgtt---
||| ||||||||||| ||||| ||||| || || || || |||||||| || ||| ||||||| ||||| || || |||||||| || || ||||| |||||     || |  ||||  |||||||  || || ||  || ||       | |||  ||||   | ||| | | ||       ||     |||    |  ||   
GGCGATTAAAGCGGCACAGCTCGGTCTTAAGACTACCTGTATCGAAAAGCGAGGCGCTCTCGGTGGTACTTGTCTTAACGTCGGCTGTATTCCTTCAAAGgtg---attttagaaactccttttccgattacc-ttgattcgtcggaaattttctccgattttca-ttcgtctcctgtggaacttgctcgttgatcatcatttag

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv05s0020g00380.t01 (Vitis vinifera), 5'ss of exon 1
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgttta----aatcttgtgttgtt
 ||||||||||| || ||||| ||||| || ||||| || ||||| || || |||||||||||||||||||| ||||||||||| || || |||||||||||    |    |        ||||| ||||      ||||| ||||| | |||  |   |  | | ||  || | |  ||  |||      |  |||||||   
CGCCATTAAAGCTGCCCAGCTTGGTCTCAAGACCACCTGTATCGAGAAGCGCGGCACTCTCGGCGGTACCTGTCTCAACGTCGGTTGTATTCCTTCCAAGgtaatatagggtttccttttttttcttttttggaaatttttatttct-cttgttggatctgtggattttgttgtttgtttgatttctggcgactttgtgtt---

upper sequence: GLYMA07G36040.1 (Glycine max), 5'ss of exon 1
lower sequence: EDP01871 (Chlamydomonas reinhardtii), 5'ss of exon 2
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaacc-gcttttccttttcccctttttttgtttctgcgtgtc---tgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt
||| || || || |||||||||||||| |    | | ||| | ||    |||||| | || ||||| |||||||||||||| || |||||||| ||||||||       |         || ||    |         |   |     | | | |   ||| |  || ||  |     || |   |   | |  | ||   |  
GGCTATCAAGGCCGCGCAGCTGGGTCTCAGCGTCGCCTGCGTGGAGGGGCGTGGCGCGCTGGGCGGCACCTGCCTCAACGTGGGCTGCATCCCCTCCAAGgtgtggcgccgggggctgagcattaaggtggtgggaggtggggccgaggggaggccaatggcagccgcaa--cgggggctgggatggggacacgtagtaggg--

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|298173817|gb|HO017153.1|HO017153
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|16281431|gb|BI944484.1|BI944484
EST:     CTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: CTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|16997280|gb|BM086652.1|BM086652
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|213594011|gb|DB961927.1|DB961927
EST:     GTGGCACTCTCGGCGGTACCTGCCCCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|208061653|gb|GD859619.1|GD859619
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|207741667|gb|GD713966.1|GD713966
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|16282064|gb|BI944817.1|BI944817
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
EST: gi|16282493|gb|BI945047.1|BI945047
EST:     GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAG                         GCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC
genomic: GTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttc ... tttggtacagGCACTTTTGCATTCTTCCCACATGTATCATGAGGCTAAACATGCATTTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCATTAAAGCGGCGCAGCTGGGTCTGAAAACCACTTGCATCGAAAAACGTGGCACTCTCGGCGGTACCTGCCTCAACGTCGGATGCATCCCTTCCAAGgttcattttcttcaaaccgcttttccttttcccctttttttgtttctgcgtgtctgggattcgaaattcattttctagttcgtttaaatcttgtgttgtt

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