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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaatggagctttgctagaatcacaaagatgttctaacttcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGCAAGCCGGGGAAATGGGAAACGTCCAGTCGGAGGTCCTCTTACAAAAGGG

Basic information

species Selaginella moellendorffii
transcript EFJ11028
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11028 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM5G826714_T01 (Zea mays), 3'ss of exon 5
-----------------------gtaagtgaatggagctttgctag---aatcacaaagatgttctaact--tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGCAAGCCGGGGAAATGGGAAACGTCCAGTCGGAGGTCCTCTTACAAAAGGG
                         ||  |||   |  |     |    |    |  |  |  | || ||   | ||  ||||||| ||||||||||| |||||  | ||||||||||| ||  |||| |||||||||||  || | || || || || || ||| | ||  | |  |||| 
gtaagtaaacttgccatccttatagaaaagaacaaaaataaagcaacctacctcctgatgtaatttatctgtcccatttcagATGATACGGCAATGTTCTGGGGTGTAAAATTCTACAATGATCTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAGCTGCTTCTCCGCAAGGA
















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|169077319|gb|FE485621.1|FE485621
EST:     CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCA                         ATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
genomic: CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
EST: gi|169040858|gb|FE447909.1|FE447909
EST:     CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCA                         ATGACACGGCAATGTTTTGGGGGATCAAATTTTACAACGACATGCTCATGC
genomic: CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
EST: gi|169103314|gb|FE508864.1|FE508864
EST:     CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCA                         ATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
genomic: CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
EST: gi|169040859|gb|FE447910.1|FE447910
EST:     CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCA                         ATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
genomic: CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
EST: gi|169113932|gb|FE515987.1|FE515987
EST:     CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCA                         ATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC
genomic: CGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGC

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: 78

TACACGCAGTGGAATTTGGTTGTCCAGCATCCCAATTTCAACAACTTGACCGAGGCATTCAGCTTTACGTACAGGCCACTGCAAGCCTATGGATCAATCAgtaagtgaat ... tcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGCAAGCCGGGGAAATGGGAAACGTCCAGTCGGAGGTCCTCTTACAAAAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgaatggagctttgctagaatcacaaagatgttctaacttcaatcacagATGACACGGCAATGTTTTGGGGGATCAAATTCTACAACGACATGCTCATGCAAGCCGGGGAAATGGGAAACGTCCAGTCGGAGGTCCTCTTACAAAAGGG
                                     ttctaac  putative branch site (score: 78)