Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttattttccttcataagaatggttctttcgtggccttgcattaactcgctattcataatttgctttttaaattttggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG

Basic information

species Glycine max
transcript GLYMA09G12430.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 1
gtta-gttattttccttcataagaatggttcttt-cgtg-gccttgcattaactcgctattcataatttgctttttaaattttggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
|| | | |    || |  || |   |   | | | | |    |||| |  | |||   |  | || |||  || | |   |||   || ||||| |||||||| |||||||||||||| ||||||||| ||||
gtcaagctcagatcttctatcactctccctttatacatatatcttgaaacagctcaaaagcc-tagttt--ttgtgactctttctattgcagACCGAGAAGGCATTTCTGAAGCAACCCAAAGTGTTTTTATG
















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|58021442|gb|CX708183.1|CX708183
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|298185405|gb|HO030618.1|HO030618
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|58025331|gb|CX712072.1|CX712072
EST:     AGCNTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|298198041|gb|HO039580.1|HO039580
EST:     TTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: TTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|13181115|gb|BG352455.1|BG352455
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAAC--                         A-A-AGAAGGCTTTTCTGAAGCAACCAAAAGTGTTT-TATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|192303094|gb|FG994212.1|FG994212
EST:     GTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: GTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|298171592|gb|HO021184.1|HO021184
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|120532484|gb|EH260617.1|EH260617
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|298195925|gb|HO044316.1|HO044316
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|15336926|gb|BI497582.1|BI497582
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|298163527|gb|HO012260.1|HO012260
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|193641647|gb|FK592473.1|FK592473
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAA
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAA
EST: gi|11414033|gb|BF425973.1|BF425973
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|151404874|gb|EV274688.1|EV274688
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
EST: gi|31464691|gb|CD406704.1|CD406704
EST:     AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGCCAGAACAA                         ACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
genomic: AGCCTGCAAGCTTCGCCGTTTGAAACAGTGCCTCAACCATGGCAGAACAAgttagttatt ... tggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggccttgcattaactcgctattcataatttgctttttaaattttggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG
         cattaac  putative branch site (score: 2)
                    tattcataatttgctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttattttccttcataagaatggttctttcgtggccttgcattaactcgctattcataatttgctttttaaattttggcttacagACAGAGAAGGCTTTTCTGAAGCAACCAAAAGTGTTTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA