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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttcacttttcttcttttcttgaaggtttttctcaagctggatttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTCTAACATTGTTTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ20512
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20512 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------gtaccttcacttttcttcttttct------tgaaggtttttctcaagctggat-----ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTCTAACATTGTTTCAAG
                                || |  | | | | |  ||||| |        | | |     |   |||| ||     |||||   |||||  ||    |  | || ||| |||| |||||||| |||||||||||||| || |||||||||||
tgggatttcatcgagatctattctgtaaaattgtccgattagtgtgccgcttttttgatgtgcaatgatgccaatatggctgtatcgttcttttgtgcagTCGACTGCGTGTAATTGCAGAGTTACGGCACGGAGATTTATTTCATTCTTCAAATATTGTTTCAAG
















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|169064442|gb|FE472109.1|FE472109
EST:     TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAG                         TCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
genomic: TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
EST: gi|169093559|gb|FE495762.1|FE495762
EST:     TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAG                         TCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
genomic: TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
EST: gi|169083269|gb|FE491885.1|FE491885
EST:     TCAGGCCTTGAGGACTTTAGATCTATTCTCGCTGGCTTCACCAGATATAG                         TCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
genomic: TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
EST: gi|169077265|gb|FE485151.1|FE485151
EST:     TCAGGCCTTGAGGACTTTAGATCTATTCTCGCTGGCTTCACCAGATATAG                         TCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCA
genomic: TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCA
EST: gi|169111050|gb|FE512471.1|FE512471
EST:     TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAG                         TCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC
genomic: TCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTC

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), 35 (downstream exon)
Score: 46

TTGTTAAAAAGGAGAAAGACGAAGAAGCCTGTGGTGGGTTTAATCAACCTTCGGGCCTTGAGGACTTTAGATCCATTCTCGCTGGCTTCACCAGATATAGgtaccttcac ... ttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTCTAACATTGTTTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcacttttcttcttttcttgaaggtttttctcaagctggatttttgcttagTCGTTTGGAGCTGGTGGCTGAGCTACGACACGGAGACTTATTTCATTCTTCTAACATTGTTTCAAG
                                            tttttgctt  CT-rich tract
                                           attttt  TA-rich tract