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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataatttgatcattactttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct...

Basic information

species Glycine max
transcript GLYMA08G37270.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 10
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataatttgatcattactttaccagt-gtttcaatagtcacagactgaga-tggaagggatctgtgtcactgtctgtttttct
||||||||  || ||||| |||||    ||||| ||||| || ||||||||||| || || || || || |||||||| |||||||||||| | ||||||||    |            | | || |  |   || ||||    |    |   | | |   | ||  || |  ||  |  || | | |||  | |       
GTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTAAGCAGgtctgtagcacttctgatccctgatgt--tttatattttatagatcacattgtttgcctttgtcttggactctaaaaggactttctaacttccag-------

upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G135283_T02 (Zea mays), 5'ss of exon 9
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataat-ttgatcattactttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct
|||||| |  || |||||||||||    ||||| || ||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||| | || |||||   |   |  |     ||||  | || |  ||||   |       | |   | | |      ||||       |  | | | | |   |          
GTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCAAACAGgtctgc---tccacttattcatgttgtttaatattatcctttattcatattgtttgcctttttatgagtctctcagcttttattttatatttcag------

upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 5'ss of exon 2
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtgga---gaagatcataatttgatcattactttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct
||||||||| |||||||||||||| || ||||| || |||||||| ||| ||| ||||||||| ||||| ||| |||| ||||||||||| ||||| |||||      |  |    ||  ||  | || |  | ||     |  || | |||   | | || | |   |   ||  |||    |    |   |||  | |   
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgtttgctggctggataattttcatatattaatgcgcattacattttttttgtgg-caaaaaggaaagggggggggggaagaaagaaaatctaatatg--

upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 10
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacac-----aagtggagaagat-cataatttgat---cattactttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct
||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||| |||||            |||| ||  | ||||  || ||   |||||| ||     | |||   | ||  || |  |  | |   |||    |    | ||           
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctctggctggataattttcatatattaatgcgcattacatttttttttttttttttgtggcaaaaaggaaagagggggggggggaagaatgaa---------

upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 5'ss of exon 3
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacac-----aagtggagaagat-cataatttgat---cattac-tttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct
||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||||||||| ||||| ||| |||| ||||||||||| ||||| |||||            |||| ||  | ||||  || ||   |||||| |||     | |||   | |  | |     ||| ||  |||    |    |  |           
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgttctctggctggataattttcatatattaatgcgcattacatttttttttttttttgtggcaaaaaggaaagaggggggggggggggaaaaaaga----------

upper sequence: GLYMA08G37270.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 10
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataatttgatcattactttac-cagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct-
||||||||| |||||||||||||| || ||||| || |||||||| ||| ||| ||||||||| ||||| ||| |||| ||||||||||| ||||| |||||      |  |    ||| ||  ||     |||| |   |      |||   | ||  || |  |  | ||  ||||   |  | |   |||  | | |  
GTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGAAACAGgtctgtttgctggctggataatt-ttcatatattaatgcgcattacattttttttgtggcaaaaaggaa-gggggggagaagaatgaaaatctaatatgcca

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|20813250|gb|BQ297728.1|BQ297728
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|6134799|gb|AW133192.1|AW133192
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|9900480|gb|BE609448.1|BE609448
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|120496684|gb|EH224851.1|EH224851
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|9439993|gb|BE440504.1|BE440504
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|120496962|gb|EH225129.1|EH225129
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|120532861|gb|EH260994.1|EH260994
EST:     CTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: CTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|17518985|gb|BM188027.1|BM188027
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|7326943|gb|AW620741.1|AW620741
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|17400278|gb|BM177060.1|BM177060
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAG                         GCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
EST: gi|22524932|gb|BU083743.1|BU083743
EST:     GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAATTTT                         TTCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC
genomic: GTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagt ... gtgaatgcagGCCACTACTCCCGAATATAGAGCATATCAAGAGCAAGTTCTCAGCAACAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGACTACGAAGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGTGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCGTTGAAGCAGgtacacaagtggagaagatcataatttgatcattactttaccagtgtttcaatagtcacagactgagatggaagggatctgtgtcactgtctgtttttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC