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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtcattccctctttcagtgcattcgtgctgtgtggtagagctaactttgctcggttggtatag

Basic information

species Selaginella moellendorffii
transcript EFJ29073
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaa--gtcgtca------ttccctctttcagtgcattcgt-gctgtgtggtagagctaactttgctcggttggtatag----------------------------
||| ||||||||| |||||||||||||||| ||||| || ||||||||||| ||||| |||||||| |||||||| |||||| || |||| ||||| || ||||  | | | |      || | ||||| ||| |   | |  |    ||||      |  |  |||| |      ||                             
AGTCATGACCAAGTTGATCCCCAGGAACACCGTCATCCCCACCAAGAAGTCCCAGGTGTTCACCACCTACCAGGATCAGCAGACAACCGTCTCCATCCAGgtaacagacataagcaaactttcttctttgagtcctgacattacatcctggtcagaaaatttcagctcagaccacctaacgcctctgaatctcgccttgtggtgtag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaa--gtcgtcattccctctttcagtgcattc------gtgctgtgtggtagagctaactttgctcggttggtatag---------------------
||| ||||||||| ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||| |  | || ||||| || ||||  ||      |||     |   || ||||      ||    || || |  | ||    ||  | ||| || | |                     
AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaacggttactgctcctctgctgcctgaattctccattgtcagctgcgggattggtagtaatgacctgtttgttttgtcctgtaatccataaatacag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagt-----cgtcat--tccctctttcagtgcatt-cgtgctgtgtggtagagctaactttgctcggttggtatag---------------------
||| ||||||||| ||||||| |||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||| |  | || ||||| || |||||      | || |  |||    |||  ||||||    |||| ||| | |     | | ||  | ||| || | |                     
AGTCATGACCAAGTTGATCCCGAGGAACACTGTCATCCCGACCAAGAAGTCGCAGGTGTTCACCACCTACCAGGACCAGCAGACCACTGTCTCCATCCAGgtaaggacgcgcatcctgctcctgtcttctctgcattgtcagctgcgtgcttggtagtaatatgacctgtttgttttgtcttgtgatccaaacatacag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtcattcc----ctctttcagtgcattcgtgctgtgtggtagagctaactttgctcggttgg-tatag-------------------------------------------
||| ||||| ||| |||| ||||| |||||||| || ||||||||||| ||||| || |||||||| ||||||||||||||| |  |||| |||||||| ||| |  | ||||      |    |  |||  ||  | ||   |   | |   | |  |    |||    |||                                             
AGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCGACCAAGAAATCTCAAGTGTTCACCACCTACCAGGACCAGCAGACTACCGTCTCCATTCAGgtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactatgatgggattgacttgaaacgattcactgcttttttcttaatacag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtcattccctctttc-------agtgcatt---cgtgctgtgtggtagagctaactttgctcggttggtatag---------------------------------------------
||| ||||| ||| |||| ||||| |||||||| || || |||||||| |||||||| |||||||| || |||||||||||| |  | || |||||||| ||| |  | ||||      ||        || ||||    |||| | |       |    |   |||  |  ||   |                                               
AGTCATGACAAAGTTGATTCCCAGAAACACTGTTATCCCAACCAAGAAATCTCAGGTGTTCACCACCTATCAGGACCAGCAGACTACAGTCTCCATTCAGgtatggtgccattattcaatttgcattaaagggcatgatgcgtgtttttcttctaaatctaaaatgcatgactgtagtgaactatgacggggttgactcgaattcactgctttttcttaatacag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtcattc-cctctttcagtgcattcgtgctgtgtggtagagctaactttgctcggttggtatag-------------------
 |||||||||||| |||| || ||||||||||| || ||||||||||| ||||| || ||||| || |||||||| |||||| |  |||| |||||||| |||  |         ||||  |||     | |  | | |||  | ||  |    |        |||  |                     
GGTGATGACCAAGTTGATTCCTAGGAACACTGTTATCCCGACCAAGAAATCTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaatgcaaacctcaatcaagttctacaagttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtcattccctcttt-cagtgcattcgtgctgtgtggtagagctaactttgctcggttggtatag-------------------------------------------------
 |||||||||||  |||| ||||| ||||| || || || |||||||| ||||| || ||||| || || ||||| |||||| || | ||||||||||| |||   | || |      |        | || ||   ||||   | |    ||   |  |  |    ||||                                                 
GGTGATGACCAAATTGATTCCCAGAAACACCGTTATCCCAACCAAGAAATCTCAAGTTTTCACTACCTATCAGGATCAGCAGACAACGGTGTCCATTCAGgtacaacttcttgaatgataaatgagaccttggtttggtgttacacataggacaagga-caatcctcatagtctttatcatctagcatctgtctgatctgaatctaatgctttcaaacag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: EDP06660 (Chlamydomonas reinhardtii), 5'ss of exon 6
AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgt-----------aagtcgtcattccctctttcagtgcatt-cgtgctgtgt--ggtagagctaactttgctcggttggtatag----------------
 || |||||||||||||||||| | ||||||||||| || ||||||||||| |||  |||||| || ||||||||||||||| |  |||||||||| || ||           | |     ||       | ||| |||   |||  ||||   || |  |   |  |       ||||    |                
CGTCATGACCAAGCTGATCCCCCGCAACACTGTCATCCCCACCAAGAAGTCGCAGACCTTCACTACCTACCAGGACCAGCAGACCACCGTGTCCATCCAGgtgcgcgcgcatgaggcaacgatggggaaatgcagggcacggcgtcatgtgcaaggaaccggcgaggtcatctatttggggggggggggtggcaaacaag

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|169098156|gb|FE499551.1|FE499551
EST:     CTCAGGTCTTCACCACGTACCANGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGAC
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGAC
EST: gi|169044229|gb|FE452959.1|FE452959
EST:     CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
EST: gi|169082521|gb|FE490045.1|FE490045
EST:     CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
EST: gi|169021566|gb|FE432111.1|FE432111
EST:     CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
EST: gi|169071495|gb|FE480447.1|FE480447
EST:     CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
EST: gi|169029068|gb|FE437571.1|FE437571
EST:     CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCAC                         GTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG
genomic: CTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAG

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), 28 (downstream exon)
Score: 11

AGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAAGAAGTCTCAGGTCTTCACCACGTACCAGGACCAGCAGTCAGCCGTGTCCATTCACgtaagtcgtc ... gttggtatagGTGTACGAAGGCGAGAGGAGTATGACGAAGGACAACCGCGAGCTCGGGAAGTTCGACCTCGCTGGCATTCCTCCGGCTCCACG




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