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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttgagattgtcattgttgtcacctgttgagatatatttaataactttttgttttatttccaactcaaactgattgcccttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCACAAAACTTTCTATAGAGAATGTGGAGCATCTCCTTATGAAAAGCCTATCT

Basic information

species Glycine max
transcript GLYMA09G34310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 4
--gtgttgagattgtcattgt----tgtcacctgttgagatatatttaataacttttt----gtt------ttatttccaactcaaactgat-tgcccttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCACAAAACTTTCTATAGAGAATGTGGAGCATCTCCTTATGAAAAGCCTATCT
   |||| |   | ||||| |    |||    || |  |  | ||| ||| |    ||    ||       ||||| |  |  | ||||||  |    |  ||||||| || ||||| |||||||| |||||||||||||   | |||||||| ||||| ||||||||| | ||| |||||||| |||| || ||||| ||||| |||
gtatgttaatgatatcattttcacttgtagtttgctaggcaagattcaattatccattcgcagtcaacaagttattgctgaagctaactgagatattgtatcttgcagCCGTCCTTCAGAAGATCGTACTATTCCCTTGAACATCATTGCAGAACGCACCAAACTTTCTGTGGAGGATGTGGAGTATCTTCTCATGAAGAGCCTTTCT
















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|193481310|gb|FK447815.1|FK447815
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|254314835|gb|GR829828.1|GR829828
EST:     GGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: GGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|254314836|gb|GR829829.1|GR829829
EST:     GGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: GGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|9898715|gb|BE607683.1|BE607683
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|15201585|gb|BI424950.1|BI424950
EST:     ATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: ATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|22524613|gb|BU083424.1|BU083424
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|19269301|gb|BM885557.1|BM885557
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|151412996|gb|EV282804.1|EV282804
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|193449468|gb|FK416447.1|FK416447
EST:     AAGTTGTTGGAAAAGATCGACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCAGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGC
EST: gi|58023449|gb|CX710190.1|CX710190
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|254334177|gb|GR849095.1|GR849095
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|23726775|gb|BU761390.1|BU761390
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|207781943|gb|GD750980.1|GD750980
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|298190509|gb|HO032630.1|HO032630
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|9203805|gb|BE330029.1|BE330029
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|24136736|gb|BU927246.1|BU927246
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|21888564|gb|BQ741777.1|BQ741777
EST:     GGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: GGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|254334178|gb|GR849096.1|GR849096
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|19053931|gb|BM732598.1|BM732598
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAG
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAG
EST: gi|16348569|gb|BI974164.1|BI974164
EST:     AAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|8402724|gb|BE058358.1|BE058358
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|208143212|gb|GD942846.1|GD942846
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTAATTCCCTTGAGTGT
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTA-TTCCCTTGAGTGT
EST: gi|11411664|gb|BF423675.1|BF423675
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|9902906|gb|BE611874.1|BE611874
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|120492821|gb|EH220988.1|EH220988
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCAC
EST: gi|193376162|gb|FK342555.1|FK342555
EST:     AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAG                         TCGGCCT-CG-A-GATCGAACTATT
genomic: AAGTTGTTGGAAAAGATCAACATTCTGTGTCTGATGGAGATTATATTCAGgtgttgagat ... ttacttgcagTCGGCCTTCGGAAGATCGAACTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaataactttttgttttatttccaactcaaactgattgcccttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCACAAAACTTTCTATAGAGAATGTGGAGCATCTCCTTATGAAAAGCCTATCT
                                          cccttactt  CT-rich tract
     aataactttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttgagattgtcattgttgtcacctgttgagatatatttaataactttttgttttatttccaactcaaactgattgcccttacttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGCACAAAACTTTCTATAGAGAATGTGGAGCATCTCCTTATGAAAAGCCTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA