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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagcgttgcaacgtctttacttctctaaactataagctgtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG

Basic information

species Selaginella moellendorffii
transcript EFJ18860
intron # 14
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|169074592|gb|FE480874.1|FE480874
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGANAAACTACACG                         ATTTATGCCGTGTCGATCACAATCC
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCC
EST: gi|169114143|gb|FE516822.1|FE516822
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
EST: gi|169107442|gb|FE508311.1|FE508311
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
EST: gi|169026011|gb|FE434454.1|FE434454
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCC
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCC
EST: gi|169096134|gb|FE500294.1|FE500294
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
EST: gi|169022707|gb|FE429734.1|FE429734
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
EST: gi|169027227|gb|FE436125.1|FE436125
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGANAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
EST: gi|169029737|gb|FE438344.1|FE438344
EST:     GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACG                         ATTTATGCCGTGTCGATCACAATCCGTATAGTG
genomic: GTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG

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: 32 (upstream exon), 35 (downstream exon)
Score: 21

GAGTGCATCTGATATTGTTCTAACTGAGCCCGGCCTTAGTGTGATTATCAGTGCTGTTCTTACCAGCCGTGCTATCTTCCAGCGTATGAAAAACTACACGgtaagcagcg ... gtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcagcgttgcaacgtctttacttctctaaactataagctgtctccacagATTTATGCCGTGTCGATCACAATCCGTATAGTG
                             ctctaaa  putative branch site (score: 21)
                                           ctgtctcc  putative PPT
                                taaactataa  TA-rich tract