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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC

Basic information

species Glycine max
transcript GLYMA10G02700.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 3'ss of exon 5
tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgca---atctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
 ||| |       | | || |  ||   |  | |  || |  ||  ||| ||  ||     ||    ||| ||   ||||    ||    |   ||| |  ||||||||||||| ||||||||||| |||||||| || ||||| |||||||| | ||||||||  || ||||| || || |  ||    ||||| ||| |  
-agccagctccttaagttgta--ttaatatattagctgtttcctttatgtttgaattttcacagttgattacatagatcttgatgtgccctgatcttttgtagGGTTCAAGTGTACCTTTGGTTGTTAAATGGGCTGACACTGAGAAGGAAAGACAAGCTCGAAAAGCACAAAAGGCTCAATTTCACCCATCTAATATGTCAA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g71200.1 (Oryza sativa), 3'ss of exon 5
tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttattt-ttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
      ||  |   ||    | ||| || | | |  | |   |||||     |  | | ||   |  | |  | | | ||   |  |  ||  ||    |||| || ||||| || ||||||||||||||||| ||||| |||||||||||||  || ||||  || ||||| || || |  |||   ||||| |||||  
-gataccttgtgtctgcattatattatccagttacatcccttctcaaaccccacgttatttttcatgaatatattataatctcttctgatttatttgttagGGCTCTAGTGTGCCGTTGGTTGTCAAATGGGCCGATACAGAAAAGGAAAGGCAGGCCCGAAAAGCACAAAAGGCTCAATTGCAATCATCTAATATGCCTA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G128809_T01 (Zea mays), 3'ss of exon 6
tagctactcatacatga-tgaaaattgt-caattaaattgc-taactcaat--gattatataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
||     ||||  ||   |     ||||  | ||  ||    ||  | | |    || |  ||  ||||  |  |   ||    |||| |||||   |     |||||||||||||||| ||||||||||||||||| || |||||||||||||||| ||||||||  || |||||| | |  | |||   ||||||||||  | 
taatagatcattgataccttggccttgtatagttgtatgatatagattacttcagttctgaaatctcatgaatctaacatggcttggtcattttggtt-----agGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAAGCTCGAAAAGCGCAAAAATCTCCATTCCAGTCTTCTAACATGTTGA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G177001_T01 (Zea mays), 3'ss of exon 5
tagctactcatacat-gatgaaaattgtcaattaaattgctaactcaatgattatataa--attcatacaattgcaatctga--tggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
     | | |||| | | |      ||  | | |       |  ||    |||  || |  | | | |||| |  ||  ||   |||| ||||||  |     |||||||||||||||| ||||||||||||||||| || ||||||||||||||||  |||||||  || |||||||| || | |||   ||||||||||  | 
atatcattgataccttggtcttgtatgatattgatcacttcagttctgaaatttcatgaccagttacacaaatctaacatgccctggtcatttttgtt-----agGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G005459_T01 (Zea mays), 3'ss of exon 5
--tagctactcatacat--gatgaaaattgtcaattaaattgctaactcaatgattat-ataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
   ||||  || |   |    |  | |  | | |||  |   || | |  ||||  ||  || ||   |   ||  |||       | | |  |   || |  ||||||| || || || ||||||||||||||||| ||||| |||||||||||||  ||||| |  || |||||||| ||||| ||  | ||| | || ||  
taaagctcttctttttttcattttagacagcccatttgac-acttattatatgaacattgtacatatttgatatcccaacg----agctctaatatattttgtagGGTTCTAGCGTGCCATTGGTTGTCAAATGGGCTGATACAGAAAAGGAAAGGCAGGCTCGGAAAGCACAAAAAGCTCAGTCACAGCTATCTCATATACCCA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: AT4G03110.1 (Arabidopsis thaliana), 3'ss of exon 5
tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
              | ||     |||  | ||  |   || ||    ||   || |  | |   | |||| ||   |  |  || |  ||   |    ||||||||| ||||||||| ||||||||||||||||| || |||   ||||| |   |  ||||   |||||| || || || ||  |  |     |   | 
-------------gtaattgcttttgctactttgaaaacttaccgtttgtaaatctgtagtgtgaaaattccatcatttttcttttggttttcttcttagGGTTCAACTGTTCCTTTAGTTGTCAAATGGGCAGACACAGAACGAGAAAGACACACAAGAAGACTTCAAAAGGCTCAATCTCACATCGCCCGACTAGGGA

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G03457.2 (Arabidopsis thaliana), 3'ss of exon 5
-tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttatttttccttctac-agGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
 ||  | || ||  |     |    | || |  |   |  | | |  || |  |  |  ||  | |   |  |||| | |   |  ||||| |||||   ||||  ||| |||||||||| |||| ||||||||||| || ||||||||||| | |||||||||   || |||||  || || || || || |   |    |
gtatgtgcttat-tacatatacttctctcgaacattcttgttattttataaagacttgtatggagagtgtgacaatatcacattctttttttcttcttttagGGAGCAAATGTTCCTTTGATTGTTAAATGGGCAGACACAGAAAAGGAAAGACAAGCTCGAAGACTTCTAAAAGTTCAATCTCATGTCTCCAGACTCGATC

upper sequence: GLYMA10G02700.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0104g01150.t01 (Vitis vinifera), 3'ss of exon 5
tagctactcatacatgatgaaaattgtcaattaaattgctaactcaatgattatataaattcatacaattgcaatctgatggttatttttccttctac-agGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
|  | | |  |      ||  | | ||  |||       ||    ||||   |  |  ||||    | | |  ||||||   ||| |||   ||  |  ||||||||||||||||| | |||||||||||||| ||||||||||||||||| | |||||| | |||||| ||||| || || || |  |||||  ||||  
tccccagttctgtgaagtggga-tagtggatttctgccttataaaaatggagaagttgattcgatgattggttatctgaccattagtttctgttgcattagGGTTCAAGTGTTCCTCTAGTTGTCAAATGGGCTGATACTGAAAAGGAAAGACAAGCTCGGAAGGCTCAGAAAGCTCAATCTCAGGCATCTAATTTGCCAA

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|58016439|gb|CX703181.1|CX703181
EST:     GAAAACATAC-ATGGGAG                         GGTTCAAGTGTTCCTTTGGTNGTCAAATGGGCAGATACTGAAAAGGAAAG
genomic: GAAAACATACAAT-GGAGgttggtgttt ... ccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgattatataaattcatacaattgcaatctgatggttatttttccttctacagGGTTCAAGTGTTCCTTTGGTTGTCAAATGGGCAGATACTGAAAAGGAAAGGCTAGCTCGAAGGGCTCAAAAAGCACAGTCCCAAGTTTCTAACATGCCGC
                            atctgat  putative branch site (score: 4)
                                     ttatttttccttctac  putative PPT
     ttatataaattcatac  TA-rich tract