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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggccgatttgtaggagatttcgaggagagaatttctggtttcctggggagtcgtgagaattgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG

Basic information

species Selaginella moellendorffii
transcript EFJ23777
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 1
----------------------gtatggcc-gatttgtaggagatt--tcgaggagagaatttctggtttcctggggagtcgtgagaattgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG
                      | |      ||| ||| |     |  || ||    || || |||  ||  | |   |   ||  | ||| | ||       ||||| ||||||||||||||||||| ||| || || || |||||  | ||||| || || |||||| ||||||||   ||||||||| ||||||| |
tggcgtgaattgcgttgaacctgcacaattagatctgtggagttctattccagtgacgatttactgtatttatagcatgctatggcacttggtttt-------gcagTGCCGTTTGAAGAGGATGACAAGGATCCGAGGATCTGGTTCCTCGATCATAATTACCACGAATCGATGTTTTCCATGTTCAAGAGGATCAACG

upper sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 1
----------------gtatggccgatttgtaggagatttcgaggagagaatttctggtttcctggggagtcgtgagaattgttcttcct--tcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG
                |||      | |   || |  ||   | | | |   || |   || |     | | ||  || || || ||  |  | || |||| || ||||| ||||||||||  ||| ||||||| |||||| | ||||||||||| |||||  |||||||| | ||||||||| | || ||||
catttgattttgcacagtacattacactgtgagcatgttcataagtgcgttgttgttacttgcacatcacttgtttgactttttgtttgtggttttacagTGCCTTTTGAGGAGGATGACAAAGACACAAGCATATGGTTTCTTGATCACAACTACCACGAGTCGATGTTTCACATGTTCAAGAGAATTAATG

upper sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------gtatggccgat-ttgtaggaga--tttcgaggagagaatttctggtttcctggggagtcgtgagaa----ttgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG
            ||||| |  | |     || |  | |  |  |||    |  || || | |  | | |||||  ||    |||   |      ||| ||| || ||||| ||||||||||  ||||||||||| |||||| | ||||||||||| || ||  | |||||  | ||||||||| | || ||||
tgcttgcttatctatggacactgtcactagaaacctctttaatagatggatgttgtttacatatgaattcgtgttaacatgttgacatcttgaattgtagTGCCCTTTGAGGAGGATGACAAAGACCCAAGCATCTGGTTTCTTGATCACAACTACCATGAGTCAATGTTCCACATGTTCAAGAGAATTAATG

upper sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 1
------------gtatggccgatt-tgtaggagatttcgaggag-----agaatttctggtttcctggggagtcgtgagaattgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG
             || ||   ||  | | ||   | |  ||  |     |||||| |   ||    |  |   |   | | | |    |  |  ||||||| || |||||||| ||||||| |||||||||||| |||||| | || ||||||||||| ||| | ||||||   ||||||||| | || ||||
ccaagcggagggttagggtttatagtattggcattgttaagagggtacaagaattgccaattattggctgttgctaaatagtagggtgttgtgtttgcagTGCCCTTTGAAGAAGATGACAAGGACCCAAGCATATGGTTTCTTGACCACAACTATCATGAATCAATGTTTTCCATGTTCAAGAGAATAAATG

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), 33 (downstream exon)
Score: 38

AACTACAATCGCGTCGCCAAGGATACGCGCAAGCGAGTTCTTGGCGTGCTGCTGGGCGCTACCTTCCGGGGCCGTGTGGATATCACTAACAGCTACGCAGgtatggccga ... cttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagagaatttctggtttcctggggagtcgtgagaattgttcttccttcttgcagTACCGTTTGAAGAGGATGACAGGGACCCAAGCATTTGGTTTTTGGATCACAACTATCACGAAGCGATGTTTGATATGTTCAAGCGGATCAATG
                                    ttgttcttccttcttg  CT-rich tract
      aatttct  TA-rich tract