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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttcttttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ27071
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
--------gtgaaccttt--cttctctccagccttgatagatcttgatggatgattgac-tcaaacttttcatttcttttgt-gtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
         |  | |      | | ||| |   |   ||| |  | ||  |  || | | ||          | |||  ||| |||| |  |  |  |||||||| | |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| || |  |||
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtatctgatgttgtgtatcatcgttgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG

upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttctt---ttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
            || |    || |  || ||||   |  |     | |     | |  | |  |  || || |       | | |   | ||| |   ||||||||| ||||| || ||||| ||||| ||||| || || ||  ||||||||||||||||||| ||||| || || ||| | |  |||
gttacaatacataatcacgattatacccggcctcattttaggagaaagtccattaggattatgcgcttaatataacacactctctaattcctttttgtagATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAG

upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttcttttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
              |       | |  |    |    | | |     | ||| |   || | ||  |  ||| || | | |||  |   |        |||||||| | |||||||| ||||| ||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| || || |||
tttatggatccaaatatgttagtttgattatgatgtctaaaactaacttatgtacctttcaatctgaaattttatatttattgact-catgtgatgtgcagATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG

upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
gtgaacctttcttctctccagcc--ttgataga-----tcttgatggatgattgac--tcaaacttttcatttcttttgt----gtgtgttc-ttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
  |   |||  |||  |||      || ||  |     |||   ||| |||||| |  ||||     | |  |||  | |    |  | ||  || || |||||||||| |||||||| ||||| ||||||||||| || || || ||||| |||||||| ||||| ||| | |||||||| || || |||
--ggttcttatttcaatcccattattttatcaactgattctctgtggttgattgtccatcaacacactgacatctaatatcatagcttatttgttttcacagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG

upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------gtgaacctttcttctctccagccttgatagatcttgatggatgattgactcaaacttttcatttcttttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
                  |||   |   ||| |  | | |  ||  | | || ||  |  || | | | |||  |   | |     || |  |  ||   ||||||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||
acgagttcccaacttaacgaaaactatctctgtgta-cttgaatttaacatgttgcgt--ttaattaagactaatttctgcaaacttg-gcttcgtttcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

upper sequence: EFJ27071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtgaacctttcttctctccagccttgatagatcttgatgga---tgattgactcaaacttttcatttcttttgtgtgtgttc-ttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
          ||||     ||   | | || | |||  ||   || || |   | ||  | | |   ||||   ||||    | | | ||  |||  ||||||||  | ||||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| ||| | || || || ||||| |||
aatcatagaatgaagaacactcgacgc-agtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatttttgttcaaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 93

GTTATCTTCATCCACAATCCTCCCTTTCATCCCCATGTCTACAGCAACGGGCACATTTGCTTAGgtgaaccttt ... cttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatggatgattgactcaaacttttcatttcttttgtgtgtgttcttctcccagATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG
         gattgac  putative branch site (score: 93)
                                       tgtgttcttctccc  putative PPT
                      ttttcatttctttt  TA-rich tract