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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

Basic information

species Glycine max
transcript GLYMA16G06850.3
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcaaacaccaaatgcataatgttatccattaaataattcattagacattatcagcctgatgtatgccaaatttgttcattatttttttaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

- -caaacac
- - - - - - - tgcataa
- - - - - - - - - - - - - -ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgcc