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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgattccaatggttgcaagagtaataaactgggcccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC

Basic information

species Selaginella moellendorffii
transcript EFJ38162
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 6
---------------------------gtaagtgttgattccaatggt-tgcaagagtaataaactgggcccgctt-tcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                            | |   || || | |||| | |     ||  || |  ||      | |  ||||||| ||||||||||| |||||||||||||| ||||||||||| || ||| | | |||||||||||| |||||  |||| || ||||| | ||| || ||
gtatgtaatcctcagttcgatcatcatctcataattaatcctaatgctctagctaagcgatcacatgaaattacctgccagGTGTTTCAATGGCATCCCTTACTGAGCTCTCATTCAACTGGACTGGCTTCATCAATGCCATGATATCAAACATCTCATTCACCTACAGGAGCATTTATTC

upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtaagtgttgattccaatggttgcaagagtaat----aaactgggcccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                                ||| || | || | |||     |   ||||     |  |   |     | |||||||||| ||||||||  | |||||||||||||||||||||   || ||| | ||||| ||||| || |||||  | || || ||| ||| |||||| ||
tgtaaatagattatgtgaaaaatgcaggtaatatttgtacattttcagagtatttagtc-agtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACTGAGCTCTCGTTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATCTCCTTCACATACCGAAGCATCTATTC

upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv01s0011g00600.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------gtaagtgttgattccaatggttgcaagagtaataaac----tgggcccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                             ||| | |   |     || | ||   | || | |||     |    |  ||| ||| || ||||||||||| || ||||| || || || |||||||| || ||| | ||||| ||||| || || ||||||||||| |||||||  || || ||
gccaatatggcagactgtttggtgattttgtcgacatgtgccacataattatgtctcagtttgttcgctgaaatactgaacggctcgatttctattttagGCGTATCAATGGCATCTCTGACTGAACTTTCTTTTAACTGGACTGGCTTCATTAGTGCAATGATTTCAAATATTGCATTTACCTACAGAAGTATATATTC

upper sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------gtaagtgttgattccaatggttgcaagagtaataaactgggcccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
                                                  |  ||||||    ||| |   ||  |   |||               | |||||||||||||||||||  | |||||||| || ||||||||||  || ||| | ||||| ||||| || || ||  | || || ||||| |  ||||| ||
tgaacttgtgaattcttattcaaagctgttttccagaaatacttgattatgacagtgtttccaccatttcatgtgattttaact--tcaaaataaaatgcagGTGTGTCAATGGCATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTC

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|169057525|gb|FE464477.1|FE464477
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169055191|gb|FE462404.1|FE462404
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169098868|gb|FE502265.1|FE502265
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169086705|gb|FE494342.1|FE494342
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169104796|gb|FE505391.1|FE505391
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
EST: gi|169041079|gb|FE450366.1|FE450366
EST:     GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTG                         GTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG
genomic: GCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCG

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

CACTGGAGCCATTCTTTAGCGCAGCCGCTTCGCAGTTTATACTGGGGCAGCAAATTTCTCTGCCGCTTTGGCTCTCTCTCACGCCCGTTGTCCTTGgtaagtgttg ... ccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtgttgattccaatggttgcaagagtaataaactgggcccgctttcagGTGTGTCAATGGCATCGCTTACTGAGCTCTCGTTCAACTGGACGGGATTCGTGAGTGCCATGATATCCAACATTGCATTTACGTACAGAAACATCTACTC
        tgttgat  putative branch site (score: 21)
                                            cccgctttc  putative PPT
                              agtaataaa  TA-rich tract