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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgagacgctaggaactcatattgcttgaaattctctctcatcgttttctagcttttgggctcttttcctttgacagttcttgttgcgaagctaattcttttgacggtgctggttttggctttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTCAGGCTTGCTTGCAAGGACTCTGTCCACTGTCGAACGTCACATTCGAGAT

Basic information

species Selaginella moellendorffii
transcript EFJ23867
intron # 5
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|169075028|gb|FE482246.1|FE482246
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|70670011|gb|DN838588.1|DN838588
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169026943|gb|FE434268.1|FE434268
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169075027|gb|FE482245.1|FE482245
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169033431|gb|FE442304.1|FE442304
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169099245|gb|FE502070.1|FE502070
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169107432|gb|FE504180.1|FE504180
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169099246|gb|FE502071.1|FE502071
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169041186|gb|FE450421.1|FE450421
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGGTCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCACTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
EST: gi|169033432|gb|FE442305.1|FE442305
EST:     GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAG                         GTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC
genomic: GGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTC

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: 27 (upstream exon), 28 (downstream exon)
Score: 8

GAAGCCTACTCCCAGCACGAGGAGCTCGGGTATTTTATCATCAGGCCCGGGGGATTACTCAACAAAGAAGGCGGTCAATACAAGATCATCGCCGAACAAGgtgagttgag ... ttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTCAGGCTTGCTTGCAAGGACTCTGTCCACTGTCGAACGTCACATTCGAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttgttgcgaagctaattcttttgacggtgctggttttggctttgtctgcagGTGACAAAGGGCTGGGGACCATTGCTCGAAAGGACGTTGCAGTGATTGCTCAGGCTTGCTTGCAAGGACTCTGTCCACTGTCGAACGTCACATTCGAGAT
                      ttttgac  putative branch site (score: 8)
                                           ctttgtct  putative PPT
                taattctttt  TA-rich tract