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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatattgtcattttacctttattacatatttttcagtatgtaatgattaatactattaaatggttattatttattttaatttccctcctcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG

Basic information

species Glycine max
transcript GLYMA08G22840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 3'ss of exon 3
tttatattgtcatttt-acctttattacatatttttcagtatgtaatgattaatactattaaatggttattatttattttaatttccctcc----tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG
     || |  ||  | |  || | || | |||| | | |  ||| | |  | |  | |  |  | | ||| |      |||    |        |    |  || || | ||||| || | |||||||||||| ||||| |||||||||||||| |||||||| |  |||||||| |||||||| ||  | |||||||
----aatagggatcctcatgttaaatataaatttataaat-cgtactaacgatttgtttctatcgatcattttacccactaagcagctattgaaattgctactagATGGCAGATGCTGGCTACCACTGCTTTGCTCCTGATTGGATAGGATTTGGGTTCAGTGATATGCCACAGCCCGGATATGGATTCGACTACACAG

upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117531_T02 (Zea mays), 3'ss of exon 3
-tttatattgtcattttacctttattacatatttttcagtatgtaatgattaatactattaaatggttattatttattttaatttccctcctctta-aacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG------
 ||   | |  ||  ||   |  |  |  ||||||| |  |  |      |  |  | ||||    |||| |  |  | ||| |  | |      | || || || | ||||| || | |||||||||||||||||||||||| |||||||| |||||||| |  ||||| || |||||||| ||  | |  | ||      
cttagaactcccacgtttattacaacat-tatttttaatcacattgcatcttttgtt-ttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAGGTCAGG

upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 3
-tttatattgtcattttacctttattacatatttttcagtatgtaatgattaatactattaaatggttattatttattttaatttccctcctctta-aacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG
 ||   | |  ||  ||   |  |  |  ||||||| |  |  |      |  |  | ||||    |||| |  |  | ||| |  | |      | || || || | ||||| || | |||||||||||||||||||||||| |||||||| |||||||| |  ||||| || |||||||| ||  | |  | ||
cttagaactcccacgtttattacaacat-tatttttaatcacattgcatcttttgtt-ttaatcaattatcacatcctctaagtatcttttgaaaataaaagATGGCAGATGCTGGCTACCACTGCTTTGCACCTGACTGGATCGGATTTGGGTTCAGTGAAATGCCACAACCTGGATATGGATTCGACTTTAAAG

upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G52510.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------tttatattgt---cattttacctttattacatattttt-cagtatgtaatgattaatac-tat-taaatggttatt------atttattttaatttccctcctcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG
                           | ||||| |    || ||     | || | | | | ||    | |  ||||| | ||   ||| || |||    ||      || | || |   |||||  |  |  || ||||||| ||||| || || || |||||||||||||||||||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||
gtgctacactgaatcttgaatcatgtgtctatatgggaaacaattgtttctaatgaaagactcttatgatttccaatgaatcatgtgtatgtatatgaagcttgagtggatcttttgtgtgttcccaacaatgtaatagTTGTCAGATGCTGGATTTCATTGCTTTGCACCTGACTGGATAGGATTCGGATTCAGTGACAAACCGCAGCCTGGATACGGTTTTAATTACACAG

upper sequence: GLYMA08G22840.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g07500.t01 (Vitis vinifera), 3'ss of exon 3
tttatattgtcattttacctttattacatatttttcagtatgtaatgattaatactattaaatggt--tattatttattttaat---ttccctcctcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG
       || |   |    |  || |   ||||  |  | | |  ||     || || |   || |   ||| | ||  | ||    ||   |  |||| || || |||| ||||  ||||| ||||| ||||||||||| |||||||| |||||||||||||| || ||| |  |||||||||| ||| | |||||||
-----gatgcctactagtatgcataatggatttacctatttctgttgtcctttattaattgttgctaccattgtctaaataaaactgttttgttttcttgaatagATGTCAGATGTTGGGTTTCACTGTTTTGCACCTGATTGGATAGGCTTTGGTTTCAGTGAGAAGCCATATTCAGGATATGGATTTGACTACACAG

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|120491597|gb|EH219764.1|EH219764
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
EST: gi|20498239|gb|BQ273169.1|BQ273169
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGGTTC-ACTGCTTTGCACCTGACTGGATAGGATTGGG
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGG-TTCCACTGCTTTGCACCTGACTGGATAGGATTTGG
EST: gi|9258501|gb|BE346648.1|BE346648
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATANGATTTGGT
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
EST: gi|22540488|gb|BU090331.1|BU090331
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
EST: gi|120491643|gb|EH219810.1|EH219810
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
EST: gi|151402689|gb|EV272502.1|EV272502
EST:     TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAG                         TTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT
genomic: TTCATGGGGCCCCTACACAATCTTTTAGCTACCGAGTTGTCATGTCTCAGgttatcatgc ... tcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaatactattaaatggttattatttattttaatttccctcctcttaaacagTTGTCGGATGCAGGGTTCCACTGCTTTGCACCTGACTGGATAGGATTTGGTTTCAGTGACAAACCACAGCCAGGATATGGTTTTAATTACACAG
                              ttttaat  putative branch site (score: 3)
                          tttattttaatttccc  CT-rich tract
     aatactattaaatggt  TA-rich tract