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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgagttctctcttctcgacttgtttcaagtaagctctttgattgatcgaggttttgtttcgtttccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT

Basic information

species Selaginella moellendorffii
transcript EFJ10950
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv01s0010g02700.t01 (Vitis vinifera), 3'ss of exon 3
---gtaagctgagttctctcttctcgacttgtttcaagtaagctctttgattgatcgaggttttgtttcgtttccttaaa---cagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT
   | || |  | |  | ||     ||  |||||  | |    || |||| |  || |  |  |  |  |||| |   ||   |||||||||||||||||||||||||| ||| |||| ||  |  |||| |||||  |  | ||    |||  | | || ||||||||  |  | ||  | || |
gttgaaatcgaaatcttttccaaatgatatgtttttatt----tcattgaatcttc-atttcctcataagtttgcgggaactgcagATCTATGCGATGCCAGTGTTTGACATGTTGGAGACATTGTTGGTGAAGAATCTGAAATTCAGACCATCTTTCATGCTTCGTCTTATTACCCGCACCCTAT

upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv01s0010g02520.t01 (Vitis vinifera), 3'ss of exon 3
gtaagctgagttctctcttctcgacttgtttcaagtaa-gctctttgattg----atcgaggttttgtttc-------gtttccttaaac---agATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT
    | | | |||    |||   |  |  | ||| ||     |||| |||     || ||   ||  ||||       | ||     |||   |||| |||||||||||||||||||| ||| |||||||  | ||||| |||||| |  | ||  | |||  | | |  ||||||||  |  | ||  | || |
----gttcaattccaaattcaaaatcttctccaaatagtatgcttttatttcaatatagaatcttcatttcctcataagcttgtgggaactgcagATATATGCGATGCCAGTGTTTGACATGTTGGAAACATTGCTGGTGAAGAAACTGAAATTCACACCATCTTTCAGGCTTCGTCTTATTACCCGCACTCTAT

upper sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv01s0010g02500.t01 (Vitis vinifera), 3'ss of exon 2
gtaagctgagttctctcttctcgacttgtttcaagtaa-gctctttgattg----atcgaggttttgtttc-------gtttccttaaac---agATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT
    |   | ||||   |||   |  |  | ||| |||     ||| |||     || ||   ||  ||||       | ||     |||   |||| |||||||||||||||||||| ||| |||||||  |  |||| |||||| |  | ||  | ||| || | |  ||||||||  |  | ||  | || |
----gtgcaattctaaattcaaaatcttctccaaataatatgtttttattccaatattgaatcttcatttcctcgtaagcttgtgggaactgcagATATATGCGATGCCAGTGTTTGACATGTTGGAAACATTCTTGGTGAAGAAACTGAAATTCACACCATGTTTCAGGCTTCGTCTTATTACCCGCACTCTAT

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|169110470|gb|FE514153.1|FE514153
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169113017|gb|FE514873.1|FE514873
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169076334|gb|FE485780.1|FE485780
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169068980|gb|FE477711.1|FE477711
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169068981|gb|FE477712.1|FE477712
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169113016|gb|FE514872.1|FE514872
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
EST: gi|169095754|gb|FE498367.1|FE498367
EST:     TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAG                         ATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA
genomic: TCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAA

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), 30 (downstream exon)
Score: 22

TACCAGCTATGACAATGTTCTCCAGCGTCTCGGGAGACCCGAGTGGCTCATCGCGGCTGCCAATCTCATGGTTGTGGTTCACGTCATTGGAAGCTACCAGgtaagctgag ... ccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcaagtaagctctttgattgatcgaggttttgtttcgtttccttaaacagATCTATGCGATGCCAGTGTTTGATATGCTGGAAACCGTTCTGGTCAAGAAATTTCACTTTCCTCCAGGTGTGATTCTTCGTCTCGTCGCTCGATCACTCT
                    gattgat  putative branch site (score: 22)
                                ttttgtttcgtttcct  putative PPT
                                ttttgttt  TA-rich tract