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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaaacaccaaatgcttaatgttatccattaaatggttcattagacattatcagcctaatatatgtcaaatttgttaattatttttctaccaactcagGTTCTTTGCTTGGTTGCTATGGAAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG

Basic information

species Glycine max
transcript GLYMA19G24250.1
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