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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggattgaaagtttctcatgttctatatagttggcctcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG

Basic information

species Selaginella moellendorffii
transcript EFJ28962
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28962 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------gtagggattgaaagtttctcatgttctatatagttggcctcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG
                                                     |   |||  |   ||||   |   | | | | ||     |||   |||||||||||||||||||| ||||| ||||| |||||  |||| || ||||| ||| | ||||| ||| | ||| | ||||| ||||||||| | || || |
tggttactcttgtttgtatggtttttttggtaccatgtacaatgattgctgcttgatgatgcatgatttcatcttgacaaga-acttttttgcttaaacagGTGAAAATGATCATGGCTACCAATAGACCTGATGTTCTGGACCCTGCGCTACTGCGTCCTGGACGTCTAGACAGGAAGATTGAGATTCCGCTACCAAATG

upper sequence: EFJ28962 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------gtagggattgaaagtttctcatgttctatatagttggcct-cttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG
                                                  ||   |  |    |  |    |||   | | |     | |  || |  |||||||||||||||||||||||||| | || ||||| |||||||| || |||||  |||||||||| |||||| | ||||||||||| ||  |||| || |
gatgatgctggttgttcggttgttccttacagcttgtcctaatattttcagtgctgtgtacttgcgtagtgtgtcacaaaaaacgttcttgtttatatagGTGAAAATGATCATGGCAACCAACCGGCCTGATGTTTTGGATCCTGCACTCCTTCGACCTGGTCGGTTGGACAGGAAGATCGAGATCCCACTGCCGAATG
















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|169035134|gb|FE444917.1|FE444917
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
EST: gi|169071646|gb|FE477088.1|FE477088
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
EST: gi|169043515|gb|FE452635.1|FE452635
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCA-CCAACAGACCCGATGTCTT
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTT
EST: gi|169027922|gb|FE434929.1|FE434929
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
EST: gi|169043514|gb|FE452634.1|FE452634
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
EST: gi|169081464|gb|FE487725.1|FE487725
EST:     CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAG                         GTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC
genomic: CACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTC

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), 32 (downstream exon)
Score: 16

CGGACGGAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgtagggattg ... tcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagggattgaaagtttctcatgttctatatagttggcctcttgtccagGTGAAAATGATCATGGCAACCAACAGACCCGATGTCTTGGATCCAGCGCTCCTGAGACCTGGTCGTTTGGACCGAAAGATCGAGATTCCGTTGCCCAACG
                                                cctcttgtcc  CT-rich tract
                             ttctatata  TA-rich tract