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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtcttgtcttttctttcttttaacgtttctttgccggttttcttccttccatttcttcttttcttgtcctctttccgtagcgctctttgatttgaacttttggactgttttcttatttctattttgattttttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGATATTTTCCGCCTGAACTACGGCTAAATTGAGTTAGATCTTCTAGACTTTT

Basic information

species Selaginella moellendorffii
transcript EFJ17164
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|169066064|gb|FE473848.1|FE473848
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169029788|gb|FE438369.1|FE438369
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169066063|gb|FE473847.1|FE473847
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169029787|gb|FE438368.1|FE438368
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169076133|gb|FE484435.1|FE484435
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169108680|gb|FE512052.1|FE512052
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
EST: gi|169076134|gb|FE484436.1|FE484436
EST:     GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAG                         TTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT
genomic: GCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGAT

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), 26 (downstream exon)
Score: 9

TGTGGATTTCCAGCCCTCGGGCGCCGGCAGTGGCATGCTCGTCTTTGTCAGCGGCAGCCTTAAGCTCCAAGGCGAAGATCATCCTCTCAAGTTTAGCCAGgttcgtcttg ... tttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGATATTTTCCGCCTGAACTACGGCTAAATTGAGTTAGATCTTCTAGACTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatttgaacttttggactgttttcttatttctattttgattttttattgcagTTGTTCCATCTCATCCCGACTCCACAAGGAAGCTTCTACGTTTTCAATGATATTTTCCGCCTGAACTACGGCTAAATTGAGTTAGATCTTCTAGACTTTT
                                    ttttgat  putative branch site (score: 9)
                                          ttttttatt  CT-rich tract
                    tgttttcttatttcta  TA-rich tract