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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccatgcctatcaatctgtttcttcacaatggttttcttttctgtgaagattagctatctgtttgttgtaattgattaagtttctactttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG

Basic information

species Glycine max
transcript GLYMA10G38720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38720.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G868908_T01 (Zea mays), 3'ss of exon 1
gtccatgcctatcaatctgtttcttcacaatg-gttttcttttctgtgaagattagctatctgtttgttgtaattgattaagtttct----actttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG
  |||    | |  ||    ||     || |  |||||||  | |||  |||   |  || | | | | | || | || || ||  |    |  |   ||| |||||||| ||||||||||| |  ||||||||||| || |||||| ||||||| |||||||| ||||| |||||| | || || ||
--ccaattgtttttattctcttgcaggcagtaagttttctcctttgttgaga---ggcatttttgtttaggaaattatcaacttctttaagatatatgttttcagCCTATGTTTCATGACGGCATGAAAGAATGGAGCTGCTGCAAGCAAAGAAGCCATGATTTCAGCTTATTTTTGCAGATACCTGG

upper sequence: GLYMA10G38720.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G51700.1 (Arabidopsis thaliana), 3'ss of exon 2
gtccatgcctatcaatctgtttcttca--caatggttttcttttctgtgaagattagctatctgtttgttgtaattgattaagtttcta---ctttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG
      |    ||||  |   ||||||   | || |||   ||| | |     ||    |   | ||| |   |    | ||| | | |    |  || || |||||  | ||||| ||||| |  ||||| ||||| || |||||| |||||||||||||||| || ||||| ||||||||||||||
------gtaagtcaaatttactcttcaaatactgttttatgtttttttttttgtttcacactcgcttgctcagagaattaaagctaccaaagttcaaacttgcagCCATTTTTTCACGACGGAATGAAAGAGTGGAGCTGCTGCAAGCAAAGAAGTCATGATTTCAGTTTGTTCTTGGAAATTCCAGG

upper sequence: GLYMA10G38720.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0022g02040.t01 (Vitis vinifera), 3'ss of exon 1
----gtccatgcctatcaatctgtttcttcacaatggttttcttttctgtgaagattagct-atctgtttgttgtaattgattaagtttctactttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG
    ||   ||| | | ||| |   | |  | | |  |||||   | |   | |  ||  | || || |  || | |||  ||    | ||      ||||||||||| | |||||||| ||||  ||||| |||||||||||||||||||| ||||||||||| ||||| ||| | | |||||||||
ttatgtttttgcat-ttaatattagtttgtatactctttttcagctttcctatgtataattgatttgatatttctcattagtttgaatgctgt----atttccagCCTTTTTTTCATGATGGGATGAAAGAGTGGAGTTGTTGCAAGAAAAGGAGTCATGATTTCAGCTTATTTCTAGCAATTCCAGG

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|4396290|gb|AI495287.1|AI495287
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|4396290|gb|AI495287.1|AI495287
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|298190522|gb|HO032643.1|HO032643
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|298190522|gb|HO032643.1|HO032643
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|193330893|gb|FK297169.1|FK297169
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCG                         G
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGgtactctctc ... taatttccag-
EST: gi|193330893|gb|FK297169.1|FK297169
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCG                         G
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGgtactctctc ... taatttccag-
EST: gi|193330893|gb|FK297169.1|FK297169
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCG                         G
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGgtactctctc ... taatttccag-
EST: gi|193330893|gb|FK297169.1|FK297169
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCG                         G
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGgtactctctc ... taatttccag-
EST: gi|151397809|gb|EV267682.1|EV267682
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|151397809|gb|EV267682.1|EV267682
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|192323948|gb|FK015684.1|FK015684
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca
EST: gi|192323948|gb|FK015684.1|FK015684
EST:     TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTCGGG                        
genomic: TGTTCTCCGAGGACGACAACCCCGACGGTTGCTGTCGATACCATGATTC--Ggtactctctc ... taatttcca


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagattagctatctgtttgttgtaattgattaagtttctactttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG
                                          ctttaat  putative branch site (score: 4)
                                    tttctacttt  CT-rich tract
                        taattgattaagtttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccatgcctatcaatctgtttcttcacaatggttttcttttctgtgaagattagctatctgtttgttgtaattgattaagtttctactttaatttccagCCTATATTTCATGACGGGACAAAAGAATGGAGTTGTTGCAAGAAAAGAAGTCATGATTTTAGCTTGTTTTTGGAAATTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- -catgcct
- - - - - - - - - - -tcttcac
- - - - - - - - - - - - - - - - - - - - ttctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt