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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcgtgggatttggcattggatctatagcggttgcccgatttctcacgcattttcttttccattccctctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATCCTCAAGCGGCTCTTCATGAGCAAAACCAACCAGCCGCCAGTGTCCCTCT

Basic information

species Selaginella moellendorffii
transcript EFJ22685
intron # 2
splice site 3'
intron type U2

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|169052996|gb|FE460711.1|FE460711
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169099479|gb|FE500510.1|FE500510
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|70671039|gb|DN839616.1|DN839616
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169076248|gb|FE485694.1|FE485694
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGGTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169099478|gb|FE500509.1|FE500509
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169035084|gb|FE445920.1|FE445920
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGGTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC

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: 53

GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATCCTCAAGCGGCTCTTCATGAGCAAAACCAACCAGCCGCCAGTGTCCCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagcggttgcccgatttctcacgcattttcttttccattccctctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATCCTCAAGCGGCTCTTCATGAGCAAAACCAACCAGCCGCCAGTGTCCCTCT
                  ttctcac  putative branch site (score: 53)
                 tttctcacgcattttc  CT-rich tract
                           attttctttt  TA-rich tract