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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgattccaatggttacaggagtaataagctgggcccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC

Basic information

species Selaginella moellendorffii
transcript EFJ15759
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 6
---------------------------gtaagtgttgattccaatggt-tacaggagtaataagctgggcccgatt-tcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                            | |   || || | |||| | ||    ||  || |  ||        |  ||||||| ||||||||||| |||||||||||||| ||||||||||| || ||| | | |||||||||||| |||||  |||| || ||||| | ||| || ||
gtatgtaatcctcagttcgatcatcatctcataattaatcctaatgctctagctaagcgatcacatgaaattacctgccagGTGTTTCAATGGCATCCCTTACTGAGCTCTCATTCAACTGGACTGGCTTCATCAATGCCATGATATCAAACATCTCATTCACCTACAGGAGCATTTATTC

upper sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtaagtgttgattccaatgg---ttacaggagtaataagctgggcccgattt-cagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                                ||| || | || | |||   |||    | |  |         |  || | |||||||||| ||||||||  | |||||||||||||||||||||   || ||| | ||||| ||||| || |||||  | || || ||| ||| |||||| ||
tgtaaatagattatgtgaaaaatgcaggtaatatttgtacattttcagagtatttagtc-agtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACTGAGCTCTCGTTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATCTCCTTCACATACCGAAGCATCTATTC

upper sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv01s0011g00600.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------gtaagtgttgattccaatggttacaggagtaataagc----tgggcccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                             ||| | |   |     || |  | | | || | | |     |    | |||| ||| || ||||||||||| || ||||| || || || |||||||| || ||| | ||||| ||||| || || ||||||||||| |||||||  || || ||
gccaatatggcagactgtttggtgattttgtcgacatgtgccacataattatgtctcagtttgttcgctgaaatactgaacggctcgatttctattttagGCGTATCAATGGCATCTCTGACTGAACTTTCTTTTAACTGGACTGGCTTCATTAGTGCAATGATTTCAAATATTGCATTTACCTACAGAAGTATATATTC

upper sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------gtaagtgttgattccaatggttacaggagtaataagctgggcccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                                  |  ||||||    ||| |  | |   || |   |           | | |||||||||||||||||||  | |||||||| || ||||||||||  || ||| | ||||| ||||| || || ||  | || || ||||| |  ||||| ||
tgaacttgtgaattcttattcaaagctgttttccagaaatacttgattatgacagtgtttccaccatt--tcatgtgattttaacttcaaaataaaatgcagGTGTGTCAATGGCATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTC

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|169066747|gb|FE473306.1|FE473306
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169022180|gb|FE430983.1|FE430983
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGG
EST: gi|169102812|gb|FE503981.1|FE503981
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169061769|gb|FE470687.1|FE470687
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169034732|gb|FE445611.1|FE445611
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169071110|gb|FE477813.1|FE477813
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169030839|gb|FE438146.1|FE438146
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169021615|gb|FE432134.1|FE432134
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCCTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTC
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTC
EST: gi|169041080|gb|FE450367.1|FE450367
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169098869|gb|FE502266.1|FE502266
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGGTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGAC
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGAC
EST: gi|169063344|gb|FE472178.1|FE472178
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169086706|gb|FE494343.1|FE494343
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169104797|gb|FE505392.1|FE505392
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCT
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCT
EST: gi|169075445|gb|FE483079.1|FE483079
EST:     CAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCNGT-GTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: CAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCC-GTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169055908|gb|FE465109.1|FE465109
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 30

CACTGGAGCCATTCTTTAGCGCAGCCGCTTCGCAGTTTATACTGGGGCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgttgattccaatggttacaggagtaataagctgggcccgatttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
        tgttgat  putative branch site (score: 30)
                                 agtaataa  TA-rich tract