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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctggatacataatcccatcttatctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

Basic information

species Glycine max
transcript GLYMA20G38740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctgga-tacataatcccatctta-tctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
     |||    || ||   |||  ||       || |   | || |   |||| |  | ||||||  | ||| | |  | || ||| | |   | |  ||||| ||||| ||||| ||||||||||| ||||| |||||||||||||| || || ||||| ||||| |||||||| |||||||| || ||||||||||| |
-gacatatcgatgtacatattatgtttatttttttatagagtata-tattatgttattgatatgctttactactttactcaatattaatgttgctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT

upper sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 2
-------ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctggatacataatcccatcttatctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
        || | |  |   ||||   | |  ||| ||   ||    ||  |    ||||   ||||| |      ||  ||||    | || | | || |   ||||| ||||| ||||| ||||||||||| ||||| ||||| |||||||| || |||||||||||||| ||||| || ||||||||||| ||||||||||| |
catatgtgtgataaaataacttcagactgtc-ttgtaag--tatctgctccagat-catgcggaagttgtttcatgtat-taatgatgtattgttttttatg--tagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACCTTTGGAATCAAGGGAGGTGCAGCTGGAGGTGGGTACAGCCAAGTTATACCCATGGATGAGT

upper sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
ctggttatttgggttcaagatattattgaaaaactacaatctt-taatcgcatgtcaaagttatgctggatacataatcccatcttatctctttttg-ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
         |    ||  | | | ||| |  | ||     ||| |  | || | |  |     | ||   |   || |    | | |  | || ||| |||||| || || || ||||| ||||| || |||||||| || |||||||| ||||||||||||||||||||||| ||||| || || ||||| |||||||| |
--------gttctctcttgctttcatttattagcttatgccttatgcttgcttttggacaaacttctctctttgtattgatttgtgaagtgttgttgcttagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT

upper sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctggatacataatccca---tcttatctctttttg---ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
         ||| | ||   | | |||  |  |   ||||  |       ||| |  |  ||     | ||  ||||  ||   |  | |||  || ||   |||||| ||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||| || || ||||| ||||||||||| || |
------gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT

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|7233770|gb|AW569113.1|AW569113
EST:     CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAG                         GTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA
genomic: CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAGgtaatccttt ... tttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA
EST: gi|151393904|gb|EV263775.1|EV263775
EST:     CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAG                         GTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA
genomic: CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAGgtaatccttt ... tttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA
EST: gi|5752485|gb|AI959772.1|AI959772
EST:     CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAG                         GTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA
genomic: CTACTACAGTGGGGCTCTGTCAAGCTTTAGGTGCTTTTCTTGATAAAAAGgtaatccttt ... tttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgcatgtcaaagttatgctggatacataatcccatcttatctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT
 ctttaat  putative branch site (score: 4)
                               tcccatcttatctctt  putative PPT
                       atacataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctggatacataatcccatcttatctctttttgttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - -gaaaaac
- - - - - - - - - - - - - - - - - - - - - - - - gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgga