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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

Basic information

species Glycine max
transcript GLYMA16G06850.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------aagcaaacaccaaat------gcataatgtta--tccattaaataattcattagacattatcagcctgatgtatgccaa-------atttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                                    |   |||||  ||||      |   || |  |  |||||   | | ||         ||  |   ||  |   |||  |       || | || | ||  |||     | | |||||||||||| | || || ||||| |||||| | ||||| |  || |||||||| ||||||||||||||||||
gcaagtgtttacatttgaaatatttgtctgttgtgaagaaaaacatgaaatttccttgttgaaagccacctccatatgacatttttccttgtttttccttgcttgtaactgcagatacttttatgtattaactaagtttagtgtaccacagGTTCTTTGCCTTGTCGCCATGGAGAAACCAATCTCTCTTAAACCCGAGCACATCCGGGATGAGAAAGTGAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------aagcaaacaccaaatgcataatgtta-tccattaaataattcattagacattatcagc-----ctgatgtatgc-caaatttgttcattatttttttaccaactc--agGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                        |  | | ||||     | ||  | || ||   ||  ||  | |||   | || |      |  |||  | |    |||   | | |   ||  ||  |      ||||||||||| | ||||| ||||| |||||| | ||||| |  |||||||| || ||||||||||||||||||
gcaagtatacctgagatacttttcctgataacaaaacttcattggaaatctatgtgattgtttttcagagtctctctgtaagttcaaatgctttcatgtattgactaactgagttcataatactctgtagGTTCTTTGCCTTGTTGCCATGGAGAAACCAATATCTCTTAAACCTGAGCATATCCGGGATGAGAAAGTGAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 9
aagcaaacacca-aatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcattatttttttaccaact--cagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
      |  |||    | || ||   |    || ||||   | ||  |  |       ||  |   | | | | ||    |   |  ||||  |  ||  ||||| |||||| ||||||| ||||| || || || |||||||  ||||||||||| || |||||||||||||||
--ttttattccatggagtatcatagcaatgtttgaatagaac-ttgaatgtatagcctcttcttctttcaatacttacatacgctagttttcactgcttacagGTCCTTTGCCTGGTTGCCATGGAGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S192_39V6.4 (Physcomitrella patens), 3'ss of exon 9
---aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcatt--atttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
       |    | ||     | | |||||    |   |  || |||      || | |  | ||      |||  | | | |    | | | |     |  ||| |||| ||  |  | || |||||||||||| |||| ||||| |||||||| ||||||||||||||||| |||
ctctcatactttcgaagctgttgacgttattggctgtgtgtttaatt-----ctacctggataatagtaatcaatgtggctaagaggagtgtctctgtgaggcagATTCTGTGTCTTTTGGCCATGGAAAAACCAATTTCCCTCAGTCCTGAGCATATTCGGGATGAGAAAGTCAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S222_130V6.2 (Physcomitrella patens), 3'ss of exon 9
aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgt-atgccaaatttgtt--cattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
  | |    |   |  |||    |||    |    |  ||| |     ||| | |   ||  || ||  ||| |  |||   || |   |||     |  |||||||| ||  |||| || ||||| ||||| ||||||||||| ||||||||  |||||||||| ||||| |||
--gaagtttctgtaatcattggcttaag-gtggggttgttcctagcgaattgtgattatgtggttatatcaattcagttaatatgaacgtttctgtgaggcagGTTCTGTGTCTGGTAGCCATGGAGAAACCTGTTTCTCTCAGCCCTGAGCATGTTCGGGATGAAAAAGTCAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 3'ss of exon 7
-------aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
         |     | ||||| ||    |  ||    ||   ||  ||  |  | |||        |   | | ||  |  ||  | | |||| |     |  ||||| || |||||||| || ||||| ||||||||||| || || || ||||||||||||||||||||||| |||
tataatttggtccttaacaaatccacccagacatat-ctacgcaaaccagaacccgttacagattccac--aaggcagctaagtggagtgttttat----gaggcagGTGCTGTGCTTGGTGGCCATGGAGAAACCAGTTTCACTAAGTCCGGAGCACATTCGGGATGAGAAAGTCAAG

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 8
aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctg-atgtatgccaaatttgttcatt---atttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                                                       |  |  |||  |  |   || |  || |   ||     | |     ||||||||||| |||||||| |||||||||||| | ||  | || ||||| ||  |||| || ||||||||||||
-------------------------------------------------------gtatacatgcgtatccctttcgggcacttaaatgcacatgctttggcagGTTCTTTGTTTGGTTGCAATGGAAAAACCATTATCCTTGAGCCCTGAACATGTTCGCGACGAGAAAGTGAAG

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|6566164|gb|AW233801.1|AW233801
EST:     ATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: ATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|15815763|gb|BI788038.1|BI788038
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|192310375|gb|FK002255.1|FK002255
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         -TTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAG-CCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|254331186|gb|GR843305.1|GR843305
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAG-CCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|16348742|gb|BI974337.1|BI974337
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|17519559|gb|BM188601.1|BM188601
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATCTGCTGCAGgtgaggccct ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacattatcagcctgatgtatgccaaatttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
          gcctgat  putative branch site (score: 4)
                                      tttttttacc  putative PPT
                        aaatttgttcattatt  TA-rich tract