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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttgaagttatctcccggattatggtctcttaacaatattgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG

Basic information

species Selaginella moellendorffii
transcript EFJ15982
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 18
-------------------------------------------------------------------------------------------------------------------gttagttttgaagttatctcccggattatg--gtctcttaacaatatt----gtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG
                                                                                                                      | || ||||  |    |   ||  |||   | || ||| ||| |     ||   |||| ||||| ||||||||||||||||| || || ||||||||||| ||||| || || ||||| || || ||||| || || || | ||
gtgtttgtagttaacctgcctggaactttcaatgaaaaaaaaagaaagaaagtatagcaacattaatttaaattttgcgtactgctgtacatttttgcataggcgtagtggcaggaggatttctgaacatggggcagagacaatgacatttcctaataatctgaagagttgtagGTGAGTGCCAACTCAGTGTATGGATTTACGGGGGCAACAGTTGGGCAGCTGCCATGTCTTGAGATCTCTTCCAGTGTTACGAGTTTTG

upper sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S14_182V6.1 (Physcomitrella patens), 3'ss of exon 18
-----------------------------------------------------------------------------------------------------------------gttagttttgaagttatctcccggattatggtct--cttaacaatattgtgt-------cagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG
                                                                                                                    | |  | |   |    |  ||   |||||||  || |||| |||  ||         || | ||||||||||| |||||||||||||| || |||||  | || ||||| || ||||||||||| || ||||| || || |||| ||
gtgcttccaacacacctgctttagcctttaatgagaacacagatatttggaagtatcaaactattacttgcatattactgtgcgttctttctgcatcggtatagtgacggaagagaaatactcatactgggccagggtgaatggtctttctcaacattatcatggataattgtagATCAGTGCGAACTCGGTGTATGGATTCACGGGGGCAACTATAGGGCAGCTGCCATGCCTTGAAATCTCCTCCAGTGTCACCAGCTTTG
















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|169106879|gb|FE505486.1|FE505486
EST:     CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAG                         GTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTT
genomic: CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAGgttagttttg ... attgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTT
EST: gi|169049692|gb|FE459318.1|FE459318
EST:     CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAG                         GTTAGTGCGAACTCAGTCTATGGATTCACAGGCGCAACAGTTGGCCAGCTT
genomic: CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAGgttagttttg ... attgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTT
EST: gi|169019789|gb|FE426876.1|FE426876
EST:     CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAG                         GTTAGTGCGAACTCAGTCTATGGATTCACAGGCGCAACAGTTGGCCAGCTT
genomic: CCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAGgttagttttg ... attgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTT

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: 26 (upstream exon), 35 (downstream exon)
Score: 8

GAAGCTACCGATTCACTTGAAAAAGCCGTGTTGGACGGTCGGCAGCTAGCTCTCAAGgttagttttg ... attgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagttttgaagttatctcccggattatggtctcttaacaatattgtgtcagGTTAGTGCGAACTCAGTGTATGGATTCACAGGCGCAACAGTTGGCCAGCTTCCTTGCCTTGAAATTTCATCCAGCGTAACTAGCTATG
                                   tcttaac  putative branch site (score: 8)
                                       ttaacaatatt  TA-rich tract