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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
---ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
    | ||   | | | ||| |  |||  ||  |||   ||| ||  ||  ||       || |     ||||  ||        |  |  || | |  | ||||  | |||||||| || ||| | || |||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || || || ||||| ||||
tgaataatctataagtttttgtagtttatatcttttc-cttgtttgcatgtagcactgaagtag--cggcattgcttaatatgtgtggtaattctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
ttgattattgaatctttttcattttg-attgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaat-tattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
|     | ||  |||      ||| |  || | |   || |  || || | | | |   |    ||   |||  ||   || |  ||||| ||| || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || |||||||| || || ||||
tctggcagtgggtctgccctttttagtgttttcttcattaccctg-tttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccatttttttt-----ctcaattattgt-ttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
   |  |    |  |||  || |   |||||||  |||  |   |  | |||||       | |||||| || |||       || | ||||| |||  || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || ||||| ||||| || ||||
---accaggttaaatttaacaatgatattgttttctttagt---accctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttc-tcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
                         | ||||||    | |   | || |   || | || | ||   || |  |  | |     | ||||||| | || |||| || |||||||| || || ||||| |||||||| ||||| ||||||||||| || || || ||||| || |||||||| ||||| || ||||| ||||
-------------------------gtttgtttttgctaccaagttttaaagtatcagt-gtctataatatactcacattttccaatgttttt-tccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
--ttgattattgaatctttttcattttgattgtttgatttgctttga-ttcagtttaactgttgac-tcccattttttttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
         ||   |  ||   || |  | | |  | ||    |  | |||  | |  |||| ||  |  |||| | |  ||   |||   ||| |    |||||| || |||||||| || |||||||| |||||||| || || || |||||||| || ||||| ||||||||||| || || ||||| || ||||||||||
gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttat----acagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
ttgattattgaatctttttcattttgattgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaattattgtttttgttcac--agGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
||  |    ||||  |||||  ||| |    || | |    ||| |    || |  | |||| |    |  |  ||   | || || | |||  |     ||||  | ||||| || || ||||||||||||||||| || || |||||||||||||| ||||| ||||| || || || |||||  |  | || || ||| 
ttcctgcccgaattgttttctgttttacc--ttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 5
ttgattattgaatctttttcattttgattgtttgatttgctttgat-tcagtttaactgttgactcccattttt--tttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
 ||| | ||  ||  |    |  |||||  |   ||  ||  || | ||||  ||  ||||   || |||| ||    |   |||| |  | ||  |    ||||| | ||||| ||||| ||  ||||||||||||| || || ||||| || ||||||||||| ||||| || ||||| ||||| ||| | || || ||  
-tgagtttt--attgtcagaaggttgatcttagcatgcgcgatgttgtcaggatacatgttttgtctcattgttaacgtacgaattgtactgttactgtgaagGTGCTTAAAACACCAGTGTCGCTGGACATGCTTGGGCGTATCTTCAACGGATCTGGAAAACCTATTGACAACGGTCCTCCCATTTTAGCAGAAGCGTATC

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|209723248|gb|BW675195.1|BW675195
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|22931741|gb|BU548880.1|BU548880
EST:     TTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: TTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|298183011|gb|HO028274.1|HO028274
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|14259630|gb|BG882538.1|BG882538
EST:     TTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: TTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|213617416|gb|DB965231.1|DB965231
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|6567285|gb|AW234896.1|AW234896
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|5342420|gb|AI794704.1|AI794704
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|213607123|gb|DB967000.1|DB967000
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|10709431|gb|BF009155.1|BF009155
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|7589581|gb|AW705352.1|AW705352
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|213592755|gb|DB957813.1|DB957813
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
EST: gi|213602215|gb|DB958475.1|DB958475
EST:     GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAG                         GTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT
genomic: GTACATCTGGGATTGACAATAAATTTACAACTGTGCAATTTACCGGAGAGgtataaactc ... ttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtttaactgttgactcccattttttttctcaattattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT
           tgttgac  putative branch site (score: 3)
                                          tttttgttc  putative PPT
                      attttttttctcaatt  TA-rich tract