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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggccctacgctatactttaccttgtttttcactgcag

Basic information

species Selaginella moellendorffii
transcript EFJ21842
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 10
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggccctacgctatactttacct-tgtttttcactg-cag-----------------------------------------------------------------------
 |||||| | || || || || || |||||| |||| ||||| | ||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| ||||||     |||| |     ||   | ||||| |        |||  ||| |||                                                                       
CATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGgtaattgcatttcttat--taatgtttacttgattaacaccttttgctggcagtcttgctttcacatcaagttgtgcaagtgtacaatttatcatattgaaacagtaatcgatccatctttcag

upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GRMZM2G700148_T01 (Zea mays), 5'ss of exon 9
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggc-----cctacgctatactttaccttgtt--tttcactgcag------------------------------------------------------------
 |||||| | || || ||||| || |||||| |||| ||||| | ||| ||||| ||||||||||| ||||| ||||| |||||||| || || || ||||||     |||| |          |||   || | ||    ||    | |  || | |                                                            
CATGCATCTGGATGCTGAGAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTCGGTCTGgtaattgcatttcttattaatatttacttaatgccttttgctggcagtcttgcttccgcatcaagttgtgcaagtgtaaaatctaccatattgagacagtaatcgatccatctttcag

upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 9
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatgg--------atatttg-tggccctacgctatactttaccttgtttttcactgcag-------------------------------------------------------------------------------------------------------------------------------------
||||||| | || || || ||||| |||||| | |||||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||  ||||| |         ||| ||| |    | |   |   |||| | |  | ||| | | | |                                                                                                                                     
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcag

upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 9
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgta---tgg-----atatttg-tggccctacgctatactttaccttgtttttcactgcag-----------------------------------------
||||||| | || || || ||||| |||||| | || ||||| | ||| |||||||| ||||||||||||||||| || |||||||||||||||||  |||||   |||     | | ||| |    ||    |   ||||  |||||||||   |                                             
GATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCTTGgtaagttggggggcacacttgattaatctgtatttctcttt-tcttgtttttttttttttttttttttttctgtttgaagggaggggcaaggattgcatgc

upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 5'ss of exon 9
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggccctacgctatactttaccttgtttttcactgcag--------------------------------------------------------------
 |||||| | || || ||||| || |||||| |||| ||||||| ||| ||||| ||||||||| |||||||||||||||||||  ||||||| ||  ||||  |    |   |  ||     ||  |  | | |||   |   || | |                                                               
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtgagatcttgcatacccacttcctgcatctaagcttagctagaacagtaatttgttaagtatttggtagtgcattatgtggcttctcatgatgcttgttgacaacattgcag

upper sequence: EFJ21842 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 5'ss of exon 9
GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatatttgtggc----cctacg-ctatactttaccttgtttttcactgcag-------------------------------------------
 |||||| | || || ||||| || |||||| |||| ||||||| ||| ||||| ||||||||| |||||||||||||||||||  ||||||| ||  ||||  |    |   |  |    ||| |  |||  | |  |     |  |   || ||                                           
CATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCTTGgtgagatcttgcataccacttcctgcatctaagcctagctggagtagtttgtgaagtggttggtggtttctcatgatgcattttttgacaaaattacag

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|169057929|gb|FE465527.1|FE465527
EST:     TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTG                         GAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA
genomic: TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatat ... ttcactgcagGAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA
EST: gi|169095330|gb|FE496734.1|FE496734
EST:     TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTG                         GAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA
genomic: TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatat ... ttcactgcagGAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA
EST: gi|169094038|gb|FE494042.1|FE494042
EST:     TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTG                         GAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA
genomic: TTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatat ... ttcactgcagGAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 25

GATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGACTGgtatggatat ... ttcactgcagGAAAATATGACCAGAATGCTTATGGTTTCTGACGTACAAGAAAGCATAAAAAGGCATCAAGTGCAGATAATCACATCTTTGAGGGACCCGGATATAAG




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