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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgtttctttggtttcttgtagcaccaccattcttcttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTTGAGTGTGGCAACTACTCGGGAGCCGCGGATTTTCTCTACCAGTATCGGA

Basic information

species Selaginella moellendorffii
transcript EFJ05347
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ05347 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
--------------------------------------------gtactttgtttctttggtttcttgtagcacc----accattcttcttcttcg-cagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTTGAGTGTGGCAACTACTCGGGAGCCGCGGATTTTCTCTACCAGTATCGGA
                                            | | |||||    |  ||    | |  |       || ||  |||| ||    ||||||||||| |  || || || ||| | |||||||| || || ||||||||||||||||| |||||||| || || || || | ||| || |||||  |  
ctgttttagtggttttaaaagaattattctacttttggaagtttgaattttgtggtatgagtcctgtctgactatgtaaacaatgattctgctgaaacagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG
















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|169020267|gb|FE430344.1|FE430344
EST:     TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAG                         ATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
genomic: TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAGgtactttgtt ... ttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
EST: gi|169068013|gb|FE476380.1|FE476380
EST:     TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAG                         ATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
genomic: TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAGgtactttgtt ... ttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
EST: gi|169077432|gb|FE485916.1|FE485916
EST:     CCAGATGCTTCACGACCGGTACCAG                         ATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
genomic: CCAGATGCTTCACGACCGGTACCAGgtactttgtt ... ttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
EST: gi|169065807|gb|FE475931.1|FE475931
EST:     TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAG                         ATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT
genomic: TCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAGgtactttgtt ... ttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTT

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), 33 (downstream exon)
Score: 9

GGCGGCTCCCTTGATCGCCTTCCTGCAAAACCCGCAAATGACAGCGGAGCTCAAGCCCGAGAGGCAAGCCAATCTCCAGATGCTTCACGACCGGTACCAGgtactttgtt ... ttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTTGAGTGTGGCAACTACTCGGGAGCCGCGGATTTTCTCTACCAGTATCGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactttgtttctttggtttcttgtagcaccaccattcttcttcttcgcagATTGGTCCCGAGCACATCGATGCGCTCTACCAATACGCAAAGTTCCAGTTTGAGTGTGGCAACTACTCGGGAGCCGCGGATTTTCTCTACCAGTATCGGA
                                    ccaccattcttcttct  CT-rich tract
        tttgttt  TA-rich tract