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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttcttttaagttttttttcctagttttatatgtgttaatggctaagaggtctgtttttttcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGGTCATTCAAGGGCGATGGCTCTTGTGGAAAAATTCCGCAAGCGGCAACTC

Basic information

species Selaginella moellendorffii
transcript EFJ23274
intron # 1
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|169101474|gb|FE501447.1|FE501447
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169087365|gb|FE492194.1|FE492194
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169098689|gb|FE498589.1|FE498589
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169094557|gb|FE492442.1|FE492442
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169080025|gb|FE489952.1|FE489952
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169116420|gb|FE517783.1|FE517783
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCATGGCTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG
EST: gi|169027513|gb|FE433746.1|FE433746
EST:     ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCG                         GAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCATGGCTGG
genomic: ACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGG

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), 27 (downstream exon)
Score: 29

ATTCAAGCTCTTGGGGAGGGAGATAGTTGTGTGGAAGGACGGGGAAGGAAACTGGAGGGCTTTCTCGGATCAATGTCCTCACAGATTGGCTCCGTTATCGgtacgttttc ... tcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGGTCATTCAAGGGCGATGGCTCTTGTGGAAAAATTCCGCAAGCGGCAACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctagttttatatgtgttaatggctaagaggtctgtttttttcctgcacagGAAGGAAGGATTGACGAGAATGGATGGCTTCAGTGCTCTTACCACGGTTGGTCATTCAAGGGCGATGGCTCTTGTGGAAAAATTCCGCAAGCGGCAACTC
                  tgttaat  putative branch site (score: 29)
                                   tctgtttttttcctgc  putative PPT
         ttttatatgtgttaat  TA-rich tract