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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttag

Basic information

species Selaginella moellendorffii
transcript EFJ12300
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA15G16470.3 (Glycine max), 5'ss of exon 10
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgt--------------aacttgcgaacgttttcctagtttaa-acaacgtgtcctttgttttag--------
| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | ||||| ||||||||              ||||||  |  |||    |   |||| |     | |     |||||          
GTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAAAATCATACACTTTTTCACAAGgttatgatcataaaataacttgaaattgttactttgaattaatatgttatctaaaaagtttttatcctacag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA09G05180.1 (Glycine max), 5'ss of exon 12
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg------aacgtt----ttccta-gtttaaacaacgtgtccttt-----gttttag--------
| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | |||||||||||||| |    |       ||| ||    ||  || ||| ||  ||  |||  | |     |||||          
GTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAAAATCATACACTTTTCCACAAGgttatgatcataaaataactttgaaattgttacgttgaattaatatgttatctaaaaagtttttatcctatag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA07G37850.1 (Glycine max), 5'ss of exon 11
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaact--tgcgaacgttttcctagttta-aacaacgtgtcctttgttttag----------------------------
| |||||||||||| |||||||||||||||||||| ||  ||  |||||| |  || || ||    |||||  | ||||||||||||||   |  |  || |          |||| ||  | |  |   |   | ||                             
GTTTTTGTTCGGAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAATGATTGTTTCCAGAATCATACTCTTTTCCACAAGgtttttgttttgagcagaaagtagctttacaattatggattgatatgtgtacatgcaaatctgatgttttgatcatatag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GLYMA17G02800.2 (Glycine max), 5'ss of exon 11
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaac-ttgcgaacgttttcctagttta-aacaacgtgtcctttgttttag-----------------------------
| ||||||||| || |||||||||||||||||||| ||  ||  |||||| | ||| || ||    |||||  | ||||||||||||||    ||  |||           | || ||  | |  |   |   | ||                              
GTTTTTGTTCGCAAGGTGATTGAGCTGCATGACAAGTACCTGGCATATGTGAACGATTGTTTCCAGAATCATACTCTTTTCCACAAGgttttgttttgaatagaaagtagctctacaattatggattgatatgtgtacatgcaaatctgaatgttttgatcatatag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S177_52V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgt----aacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttag-----------------------------------------------------------------------------------------------------------------------------
|| ||||| ||||| |||||||| || |||||||||||| |||| ||||||||||| |||||| | ||||| || ||||| ||||||||    ||  ||   || |  || |  |||  |   |  || || |  |  |                                                                                                                              
GCCTTTGTGCGGAAGGTGATTGAACTACATGACAAATATCTGCAGTATGTCAGCGACTGCTTTTTAAATCATTCTCTTTTTCACAAGgtgagaaagctgtttac-tgctcttgattttgatcgcacgttctgttctcaacgagagaatatcatgctgaagctcccttgttttctgctcggatgcagtctggaaggatttttgtgttgaaacttaatgcttggagtgttctttgtattgaagcttagtgaataatatggaatgcag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S144_158V6.1 (Physcomitrella patens), 5'ss of exon 8
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttag--------------------------------------------------------------------
|| ||||| ||||| || |||||| | |||||||| ||| |||| ||||| ||||||||||| || || ||||||||||| ||||| || |   | ||    |||||| |||   |  | ||   | |  || | |                                                                    
GCCTTTGTGCGGAAGGTCATTGAGTTACATGACAAGTATCTGCAGTATGTGAGCGAGTGCTTCGTCAACCACTCCCTTTTTCACAAAgtga---gtgactcctttccttgttccgatgatgtcggcgtctttatcgttctctttagaaattcattagatgtgataaatgaagaactttggtgtggcgtttggttttacttgcag

upper sequence: EFJ12300 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S169_153V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcgaacgttttcctagtttaaacaacgtgtcctttgttttag---------------------------------------------------------------------------------------------------------------------------
|  ||||| || || ||||||||  |||||||||| ||| |||| |||||||||||||| ||||  ||||| || ||||| |||||||| |   |  |  | ||| |     |  ||   |  | | || ||||                                                                                                                             
GTCTTTGTGCGAAAGGTGATTGAATTGCATGACAAGTATCTGCAGTATGTCAGCGAGTGTTTTGCGAATCATTCTCTTTTTCACAAGgtga---gtaactggtttgccgcccttgactttggttgccttattttgatgttatggagggtattccgtattaacggtgccctgctttctgcttgaatgcagtctgggatgattagtgtagttcttagaaatgatttttgtgataaaatctaataactaaagtggcttgcag

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:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCATTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169111912|gb|FE510642.1|FE510642
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169079161|gb|FE490908.1|FE490908
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCATTCCCTTTTCCACAAG                         GCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGC
EST: gi|169027130|gb|FE435040.1|FE435040
EST:     ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACA-G                         GCTTTGAAAGA-GCATTTGAGGTCTTTCTGCA-CAAAG-TGTTGGGGGAAG
genomic: ATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTT-CTGCAACAAAGGTGTTGGGGGAAG

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), 35 (downstream exon)
Score: 27

GCTTTTGTTCGGAAAGTGATTGAGCTGCATGACAAATATTTGCAATATGTCAGCGAGTGCTTTGTTAATCACTCCCTTTTCCACAAGgtaacttgcg ... tttgttttagGCTTTGAAAGAAGCATTTGAGGTCTTCTGCAACAAAGGTGTTGGGGGAAGCACAAGTGCTGAGTTGCTAGCAACTTTCTGCGATAACCTCTTGAAGAAAG




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