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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctagactcttccgattcttgcagctctaatactgtggagaactttggattccagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA

Basic information

species Selaginella moellendorffii
transcript EFJ36722
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 3
-----------------------------gtactgctagactcttccgattcttgcagctctaatactgtggagaactttggat---tccagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA
                               |    ||    |     ||        |  ||||    |||    |||||| |   | |||||||| || |||||||||||||||||||||||  | ||       ||||  || || ||||| |||||||||||||||||| ||||| |||| || ||||
gtacatttcactttactgagatctttcaaagatgattatcaacaatgtatctgccttccattaatgacttggttttctttggtttaatgcagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGTGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 3
--------------------------------gtactgctagactcttccgattcttgcagctctaatactgtggagaactttggattc---cagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA
                                 |      | |   ||| | | |||    |  |||| |  | |    | |||| ||     ||||||| || |||||||||||||||||||||||  | ||       |||| ||| || ||||| |||||||||||||||||| ||||| |||| || ||||
gtatatttgatttcactgggatcttgcggaagatggcaaaaaaaatttcagctgctttt--cattaattcctttgttttcattggcttaatgtagGACTCCACCTACAAGTACTTTGAGATCATCCTTGTGGATGTTGCTCACAGCGCTATCCGCAATGACCCAAGGATCAACTGGCTCTGCAAGCCTGTGCACA

upper sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------gtactgctagactcttccgattcttgcagctctaatactgtgga----------gaactttggat-tccagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA
                              |  ||     | | || ||  | ||||| ||| | ||| |||||          |||  |||  | | ||||||||||| ||||||||||||||||| |||||  | |||||    ||  | |  |||||||||||||||||||||||||||||     | || || ||||
actgccagcgatttcacttaatttgttgtagggctttatcattgtttcgggtattgca-ctccagtaccgtggaattgaatcaggaaggttgcttgtgcagGACTCAACCTACAAGTACTTTGAGATTATCCTAGTTGACCCTCAACATGCAGTTATTCGCAAGGACCCAAGGATCAACTGGATTGTGAACCCCGTCCACA

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: 52

CCAGCTCAAGTTCCAGAGAAACTTGAGATCCGTGGCCGAGGAACGTGCTGGGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagactcttccgattcttgcagctctaatactgtggagaactttggattccagGACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA
                        ctctaat  putative branch site (score: 52)
                         tctaata  TA-rich tract