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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgtcgccttttaattttgtccatagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG

Basic information

species Selaginella moellendorffii
transcript EFJ12300
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA07G37850.1 (Glycine max), 3'ss of exon 10
------------------gtattgtgtcgccttttaattttgtccatagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                    |||     || ||||   ||  |   | ||   |  |  ||      |  |  |||| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | ||||||||||||
gtgacaatttttttttattaatttaactgcattttttattcatttgtggaaattgaaa-ttggtctcttgcttcagGTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAGAATCATACTCTTTTCCACAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA09G05180.1 (Glycine max), 3'ss of exon 11
----------------------gtattgtgtcgccttttaattttgtcca----tagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                      |||| || |  |  ||   |||||| ||    |  |  ||  |  | |  | || |   |||| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | ||||||||||||
gtaatctcctagttttctaattgtatagtataactgtt--gttttgttcatttttgaacactgaaattgatctctttttttcagGTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAAAATCATACACTTTTCCACAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA15G16470.3 (Glycine max), 3'ss of exon 9
----------------------gtattgtgtcgccttttaat-tttgtccatagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                      |||| || |  |  |    | ||  |   |  |  ||  |  | |  | || |   |||| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | ||||| ||||||
gtaatctcctaattttctaattgtatagtataactgtaatttattcattttttaacactgaaaatgatctctttttttcagGTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAAAATCATACACTTTTTCACAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA17G02800.2 (Glycine max), 3'ss of exon 10
----------------------gtattgtgtcgc-cttttaattttgtccatagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                        |||     ||  ||||  |||| |   | ||   |  |  ||     ||  |  |||| ||||||||| || |||||||||||||||||||| ||  ||  |||||| | ||| || ||    |||||  | ||||||||||||
gtgataaaaaaaataattttattaatttaactgcattttttcttttatttgtggaaattgaaa-ttggtcttttgcttcagGTTTTTGTTCGCAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAACGATTGTTTCCAGAATCATACTCTTTTCCACAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S177_52V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------gtattgtgtcgccttttaa-ttttgtccatagatgctatatcttaaat-gttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                                         || |  |          || | |||   ||   || |  |||||   | | ||    ||||| ||||| ||||| |||||||| || |||||||||||| |||| ||||||||||| |||||| | ||||| || ||||| ||||||
ttgagttacacttgtataatcgccaaattgtagagctcgacgtgtccttcgattgaggaagtcttgaatattcttg-tgcatcttcggttgctccttacagGCCTTTGTGCGGAAGGTGATTGAACTACATGACAAATATCTGCAGTATGTCAGCGACTGCTTTTTAAATCATTCTCTTTTTCACAAG

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S144_158V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gtattgtgtcgccttttaattttgtccatagatgctata-----tcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                                      |||   || |  |   |||   |   | | ||  | |      |||    | |||| | ||||| ||||| ||||| || |||||| | |||||||| ||| |||| ||||| ||||||||||| || || ||||||||||| ||||| 
agggatgctagtgcaggtgtaaagctgttttattgcaatatatggttggatagaaatgacgagaagaaatattctcatggttctctggttttcttcgcagGCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAA

upper sequence: EFJ12300 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S169_153V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------gtattgtgtcgccttttaattttgtccatagatgct---atatc-ttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
                                       |  | | |   ||  ||  |   |     ||| ||     |||  ||  || |   | ||||  ||||| || || ||||||||  |||||||||| ||| |||| |||||||||||||| ||||  ||||| || ||||| ||||||
aaagacctagttgtggttgaattagaaacttgtaagtcatcctcttttatctcataggtacttagcaggattcttaggcatcactacttgcttgtcgcagGTCTTTGTGCGAAAGGTGATTGAATTGCATGACAAGTATCTGCAGTATGTCAGCGAGTGTTTTGCGAATCATTCTCTTTTTCACAAG

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|70669089|gb|DN837666.1|DN837666
EST:     CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTTCAGGAGCAG                         GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
genomic: CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
EST: gi|169111912|gb|FE510642.1|FE510642
EST:     CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAG                         GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
genomic: CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
EST: gi|169026189|gb|FE435347.1|FE435347
EST:     CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAG                         GCTTTTGTTTCG-AAAGTGATTGAGCTGCATGACAAATATTTGCAATATGT
genomic: CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTT-CGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGT
EST: gi|169079161|gb|FE490908.1|FE490908
EST:     CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTTCAGGAGCAG                         GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
genomic: CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
EST: gi|169027130|gb|FE435040.1|FE435040
EST:     CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAG                         GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC
genomic: CCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 34 (downstream exon)
Score: 20

CACGTAACGGAGGAGGGAACTACACTAGTCAAGCAAGCTGAAGATGCGGCCAGCAGCAAAAAGGCTGATAAGAAGGATACTGTTGGTGTCCAGGAGCAGgtattgtgtc ... ttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtcgccttttaattttgtccatagatgctatatcttaaatgttctccccagGCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG
          ttttaat  putative branch site (score: 20)
                                           tgttctcccc  putative PPT
                                tatatcttaaatgtt  TA-rich tract