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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaaacaccaaatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

Basic information

species Glycine max
transcript GLYMA19G24250.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------aaacaaacaccaaat------gcttaatgtta--tccattaaatggttcattagacattatcagcctaatatatgtcaa-------atttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                                    | | |||||  ||||      | | || |  |  |||||   |   ||         ||  |   ||  ||  ||   |       || | |||| ||  |||     | | |||||||||||| | || || ||||| |||||| | ||||| |  || |||||||| ||||||||||||||||||
gcaagtgtttacatttgaaatatttgtctgttgtgaagaaaaacatgaaatttccttgttgaaagccacctccatatgacatttttccttgtttttccttgcttgtaactgcagatacttttatgtattaactaagtttagtgtaccacagGTTCTTTGCCTTGTCGCCATGGAGAAACCAATCTCTCTTAAACCCGAGCACATCCGGGATGAGAAAGTGAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------aaacaaacaccaaatgcttaatgtta-tccattaaatggttcattaga----cattatcagcctaatatatgtcaa--atttgttaattatttttctaccaactc--agGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                        |  | | ||||   | | ||  | || ||   || |||  | |||    |  | | ||   ||    | |||   |||   ||| |   ||  ||  |      ||||||||||| | ||||| ||||| |||||| | ||||| |  |||||||| || ||||||||||||||||||
gcaagtatacctgagatacttttcctgataacaaaacttcattggaaatctatgtgattgtttttcagagtctctctgtaagttcaaatgctttcatgtattgactaactgagttcataatactctgtagGTTCTTTGCCTTGTTGCCATGGAGAAACCAATATCTCTTAAACCTGAGCATATCCGGGATGAGAAAGTGAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 9
aaacaaacacca-aatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaattatttttctaccaact-cagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
      |  |||    |  | ||   |    || ||| |  | | |     || |  | |  | | |    | ||   ||      |||  ||    | ||||| |||||| ||||||| ||||| || || || |||||||  ||||||||||| || |||||||||||||||
--ttttattccatggagtatcatagcaatgtttgaatagaacttgaatgtatagcctcttcttctttcaatacttacatacgctagttttcactgcttacagGTCCTTTGCCTGGTTGCCATGGAGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: PP1S192_39V6.4 (Physcomitrella patens), 3'ss of exon 9
---aaacaaacaccaaatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaatt--atttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
     | |    | ||    || | |||||    |   || || |||      || | |  |||||    ||||  | | |||    | | |       |  ||| |||| ||  |  | || |||||||||||| |||| ||||| |||||||| ||||||||||||||||| |||
ctctcatactttcgaagctgttgacgttattggctgtgtgtttaatt-----ctacctggataatagtaatcaatgtggctaagaggagtgtctctgtgaggcagATTCTGTGTCTTTTGGCCATGGAAAAACCAATTTCCCTCAGTCCTGAGCATATTCGGGATGAGAAAGTCAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: PP1S222_130V6.2 (Physcomitrella patens), 3'ss of exon 9
aaacaaacaccaaatgcttaatgttatccattaaa-tggttcattagacattatcagcctaatat-atgtcaaatttgttaatt---atttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
     ||       |  | | ||   |    |    | |||| |     ||| | |   |    | || |||| |  ||||||    |  |||||   |   |||||||| ||  |||| || ||||| ||||| ||||||||||| ||||||||  |||||||||| ||||| |||
----gaagtttctgtaatcattggcttaaggtggggttgttcctagcgaattgtgattatgtggttatatcaattcagttaatatgaacgtttctgtgagg-cagGTTCTGTGTCTGGTAGCCATGGAGAAACCTGTTTCTCTCAGCCCTGAGCATGTTCGGGATGAAAAAGTCAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 3'ss of exon 7
aaacaaacaccaaatgcttaatg---ttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaatt--atttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
     |  |     | |||||       | |||   |    | |   |  ||  | | |    | ||    |||    | ||| |  | | || ||  |   ||||| || |||||||| || ||||| ||||||||||| || || || ||||||||||||||||||||||| |||
----tataatttggtccttaacaaatccacccagacatatctacgcaaaccagaacccgttacagattccacaaggcagctaagtggagtgttttatgagg-cagGTGCTGTGCTTGGTGGCCATGGAGAAACCAGTTTCACTAAGTCCGGAGCACATTCGGGATGAGAAAGTCAAG

upper sequence: GLYMA19G24250.3 (Glycine max), 3'ss of exon 9
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 8
aaacaaacaccaaatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                                                 |   ||  |  ||   | ||       | |||     | ||       ||||||||||| |||||||| |||||||||||| | ||  | || ||||| ||  |||| || ||||||||||||
------------------------------------------------gtatacatgcgtatccctttcgggcacttaaatgcacatgctttgg---cagGTTCTTTGTTTGGTTGCAATGGAAAAACCATTATCCTTGAGCCCTGAACATGTTCGCGACGAGAAAGTGAAG

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|18040428|gb|BM308722.1|BM308722
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATTTGCTGCAGgtaggccctg ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|254338293|gb|GR849818.1|GR849818
EST:     AATTATTCGAGATATTATTCAAAACCATTTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
genomic: AATTATTCGAGATATTATTCAAAACCATTTGCTGCAGgtaggccctg ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCAC
EST: gi|16279238|gb|BI943331.1|BI943331
EST:     AATTATTCGAGATATTATTCAAAACCATCTGCTGCAG                         GTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCA
genomic: AATTATTCGAGATATTATTCAAAACCATTTGCTGCAGgtaggccctg ... accaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacattatcagcctaatatatgtcaaatttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG
                             tgttaat  putative branch site (score: 3)
                                      tttttctacc  putative PPT
             taatatatgtcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacaaacaccaaatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

- -caaacac
- - - - - caaatgc
- - - - - - - - - - - - - -ccattaa