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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggaggaaatgagagagctagaaaaatctgttatacggagtgtttggtctcagatctttgtgcgtgtgattgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAAGGGACCGCGGACGCCGTGAGGCAGTTCACTTGGCTTTTTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ25399
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 3
-----------gtggaggaaatgagagagc-tagaaaaatctgt--tatacggag---tgtttggtctcagatcttt---gtgcgtgtgattgatgt-agGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAAGGGACCGCGGACGCCGTGAGGCAGTTCACTTGGCTTTTTGAG
               |  ||     ||| | ||||  | | |||  || ||  ||   | |        || |  |    | | |  || |  || | |||| || |||||||| ||||||||||||||| | ||||  || ||||||||||| || || || || ||||||||||||   ||||| ||||||
ataagccgaccaaaaaaaaatcttcagaacatagactagtatgtagtaaacaaagaactatactcctctaggttataaaagagtgcatgttctatttcagGTTCTTGCAGCAACCCAAACTCCAGGGGAGGCAGGTAAAAAGTGGTTTCAAGGTACTGCTGATGCTGTGAGGCAGTTCCACTGGCTCTTTGAG

upper sequence: EFJ25399 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------gtggaggaaatgagagag-ctagaaaaatctgttatacggagtgtttggtctcagatcttt---gtgcgtgtgattgatgt-agGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAAGGGACCGCGGACGCCGTGAGGCAGTTCACTTGGCTTTTTGAG
                                                                                     |       |  | | || |||  ||    |   | | | | | |        || |  |    | | |  || |  || | |||| || |||||||| ||||||||||||||| | ||||  || ||||||||||| || || || || |||||||||||    ||||| ||||||
gtatctcccatcttttacttgcttgtatttttagtcagcttatgcgtgtgtatggcttataaacaattatgcgtttagttcttaataatcttcagaaaataggctactaagtagtaaaagaagaactatactcctctaggttataaaagagtgcatgctctatttcagGTTCTTGCAGCAACCCAAACTCCAGGGGAGGCAGGTAAAAAGTGGTTTCAAGGTACTGCTGATGCAGTGAGGCAGTTTCACTGGCTCTTTGAG
















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|169087299|gb|FE491712.1|FE491712
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCANACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
EST: gi|169077503|gb|FE485948.1|FE485948
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
EST: gi|169030615|gb|FE438741.1|FE438741
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
EST: gi|169112864|gb|FE514616.1|FE514616
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
EST: gi|169071157|gb|FE478354.1|FE478354
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
EST: gi|169040694|gb|FE447329.1|FE447329
EST:     ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAG                         GTACTGGCAGCAACGCANACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA
genomic: ACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAA

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: 22

CAATCGAGTTTTCGTACTCACGCAGTTCAACTCGGCGTCGCTCAACCGCCACCTCGCTCGCACCTACAACTTCATCAATGCTGGGGAAGGCTTTGTTGAGgtggaggaaa ... attgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAAGGGACCGCGGACGCCGTGAGGCAGTTCACTTGGCTTTTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctgttatacggagtgtttggtctcagatctttgtgcgtgtgattgatgtagGTACTGGCAGCAACGCAAACTCCAGGGGAGTCTGGTATGAATTGGTTTCAAGGGACCGCGGACGCCGTGAGGCAGTTCACTTGGCTTTTTGAG
                                            gattgat  putative branch site (score: 22)
     tgttata  TA-rich tract