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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA

Basic information

species Glycine max
transcript GLYMA19G35710.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 7
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaat-actgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
               |   | ||  |    ||||  | | |  ||     | ||||| |    ||    |     |  | |  | |  |||| |||  ||||||||| |||||||| ||||||||||||||||||||||| |  |||||||| |||||||| || || || || || || ||||||||||
-------------gtttggtccctactcaacaagtgcgctttcttcag--aatgaatgaacagattctaaagtggtaaggttttatccagGGAGAGGCAGATGATAAGATTATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAA

upper sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 6
-gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
  |    |  |  |   ||||| |          ||| | || || ||||       |  |  ||    ||    |||     || | |||| |||  |||||| || |||||||| || |||||||||||||||||||| |  ||||||||||||||||| ||||| || || || || || |||||||
gtttggcttcattccaacatttacaaagtccagcgaaatgctattctgatccccatgt-ttctattctgaccccatgtttgtttgaacagGGAGAGGCAGATGACAAGATTATTGCCGTTTGTGCTGATGATCCTGAGTACAAGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAA

upper sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaa--taaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
     ||| |   ||    | |  |  |    || |||  |      | ||    | | ||||  ||    ||  || ||||  || | |||| |||||||| || || || ||||||||||| ||||| ||||| |||||| | |||||||| || ||||  |||||||| || |||||| | ||||| |
----gttagatattcaacgtacttgtcatattagtacttat---aaaagtaacagagattgaaactagaagctctttctgct--tgaatagGGTGAGAAAGACGACAAGATCATTGCTGTCTGCGCTGACGATCCAGAGTATCGCCATTACAACGACATCAGTGAGCTTCCGCCTCATCGTATGGCTGAGA

upper sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 6
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattatt---gaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
             |   |      |  | |  | |  ||||||    |||| |    ||   ||||| |    | |   || | |   | |||| ||||||||||| || || ||||| || ||||||||||||||||||||  |||| |||| ||||||||| ||||| ||||| || ||||| ||||| |
------------gtagaaaaagatgacaagatatatttcctctcccaattacttctaaaccttgaattaatcttgaccttgatta-acacagGGAGAGAAAGATGACAAGATAATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGA

upper sequence: GLYMA19G35710.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------gtaaattaaaccctctcatttcccgcaagg---caagaactcctcttttgattattgaatac-tgaataaccact-----aattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
                              | |||  ||||   ||  | |    || |    ||     | |     | || ||  | ||  || | | | | |     | ||||   ||  |  |||| ||||| ||||| || || || |||||||||||||| ||||| ||||||||||| | ||| || ||||| ||| |||||||||||||  | || ||||
gtgagggactattatgccgtactctttgacggaaaccaaactagcttgtattgatcatgttctcatattgttcgtacctaatcatccactatatgtaaatctaatgttaaatttgtaaggacctgtagGGAGAGAAGGATGACAAGATCATCGCTGTCTGTGCTGACGATCCGGAGTATAGACACTTCAAAGACATCAATGAGTTTCCTCCACATCGACTTGCCGAAA

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|193399186|gb|FK361734.1|FK361734
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGANAAAGATGATAAAATTATTGCTGT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGT
EST: gi|193487362|gb|FK451853.1|FK451853
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|9901982|gb|BE610950.1|BE610950
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCT-AGATA
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAG-TA
EST: gi|193724545|gb|FK662691.1|FK662691
EST:     GTTGCTCTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|120534409|gb|EH262542.1|EH262542
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|208040310|gb|GD840312.1|GD840312
EST:     TGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: TGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|193555433|gb|FK514310.1|FK514310
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|192301012|gb|FG990112.1|FG990112
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GAGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|22523592|gb|BU082403.1|BU082403
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|254335060|gb|GR844845.1|GR844845
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|207757093|gb|GD730051.1|GD730051
EST:     TTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTA
genomic: TTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCA-Ggtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTA
EST: gi|193536962|gb|FK490118.1|FK490118
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGGAGAAAGATGATAAAAATTATTGCTGTCTGTGCTGATGATCCTGAGT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGG-AGAAAGATGATAAAA-TTATTGCTGTCTGTGCTGATGATCCTGAGT
EST: gi|298189455|gb|HO037858.1|HO037858
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|193588246|gb|FK544037.1|FK544037
EST:     GTTGCTCTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
EST: gi|8669991|gb|BE191098.1|BE191098
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAA-TTATTG
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTG
EST: gi|17964359|gb|BM271095.1|BM271095
EST:     GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG                         GGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT
genomic: GTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAGgtaaattaaa ... tgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcctcttttgattattgaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA
        ttttgattattgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattaaaccctctcatttcccgcaaggcaagaactcctcttttgattattgaatactgaataaccactaattgtgctgatgtaaagGGGGAGAAAGATGATAAAATTATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA