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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtagtctataaagttctaaacttctaaagttctctagagttctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA

Basic information

species Selaginella moellendorffii
transcript EFJ09930
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g30200.1 (Oryza sativa), 3'ss of exon 3
-----gtacgtagtctataaagttct-----aaacttctaaagttct---ctagagttct-ctcgagttgattgaagtgtttcttttttcaacc----agGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
     | |     |||| |||||| |     | ||  | ||| |  |   ||||| |||   || |  |  ||    || || |  || ||||     ||||||||| ||| |||||| | || ||| ||||||||||||||||| | ||||||||||| ||||| | |||||| ||||||||||| || ||||||||  
tcgctgcagtgcatctagaaagttttactcaacacacccaaaatgtttggctagatttcaattcaatgttgtttgcttggttttggttgcaacttgcaagGATCCACGAACGGAGAACGACCCGTACATGGGGTTCATCTACACGACGTTCCAGGAGCGCGCCACCTCCATCTCCCACGGCAACACGGCGCGCCACGCGG

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g69080.1 (Oryza sativa), 3'ss of exon 2
--gtacg-tagtctataaagttctaaacttctaaagttctctagagttctctcgagttga-----ttgaagtgtttcttttttcaa----------ccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
   | |  |  |||||   |||||   |   |     | | ||     |  | |||  ||      || ||   ||  | |||             |||||| ||    || |||||||||||||| || || ||||||||||| |||||||| ||||| || || |||||||| || || ||||| || ||||| ||||
ttttgctctgttctattctgttctgttcacattggactgtttaagtggcaattgagcagagaaatctgtagcacttactcttttgctgcatcatttccagGACCCTAGGACAGAGAACAATCCTTATCTTGGATTCATCTACACCTCCTTCCAAGAGCGTGCGACCTTCATCTCACATGGGAACACTGCTCGCCATGCCA

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G027673_T02 (Zea mays), 3'ss of exon 2
gtacgtagtctataaagttctaaacttctaaagttctctagagttctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
||  ||| | |||  |  | ||||        | |   |  |      |      |  ||| ||   |        |  ||||||||  | || ||||  || || ||| |||| ||| |||||||||| ||||||||||| ||||| |||||||| ||||||||||| || ||||||||||
gtgagtaat-tatttacctttaaatgatgggtggttgatgcatgaacgtacgcacgcatgacgtacgtacaaacaaatgcagGATCCCAAGACGGAGACGAACCCGTACATGGGCTTCGTCTACACGTCGTTCCAGGAGCGCGCCACCTTCATCTCCCACGGCAACACGGCGCGCCACGCCA

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G852502_T01 (Zea mays), 3'ss of exon 2
---------gtacgtagtctataaagt-tctaaacttctaaagttctctagagttctctcgagttgattgaagtgtttctttttt---------caaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
           || | || | |    | | ||||  |       |   || |  | | | |    || | |  |||   || |||             ||||||||    || ||||| |||||||| || || ||||||||||| |||||||| |||||||| || |||||||| ||||| ||||| || || |||||||
atcttttgttcacttcgtttttttcttctttaaatataggctacttcttataaatatgtaggag-gactaatatgtactttctttactgtgtccttttcagGATCCTAGGACTGAGAATAATCCTTATCTTGGTTTCATCTACACCTCCTTCCAAGAGCGGGCGACCTTCATCTCACACGGGAACACTGCTCGTCACGCCA

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G180399_T01 (Zea mays), 3'ss of exon 2
------------------gtacgtagtctata-aagttctaaacttctaa----agttctctagagttctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
                  |||| | || | |  ||| ||||  || || |    |  | | |||   |     |   |   |  | ||  || ||||     ||||||||    || ||||| |||||||| || || ||||||||||| |||||||| |||||||| || ||||||||||| || ||||| || || || ||||
gatgattatttctcttttgtactttgtttttttaagatctatgctactgattataactatgtaggactaatatgtagttcctttactgagtcctttt-----cagGATCCTAGGACTGAGAATAATCCTTATCTTGGTTTCATCTACACCTCCTTCCAAGAGCGGGCGACCTTCATCTCGCATGGGAACACTGCTCGTCATGCCA

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S157_50V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------gtacgtagtctataaagttc---taaactt--ctaaagttctctagagttctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
             ||  | ||    | ||   |   |  | |   |||   ||  |    ||  ||  |  || |      ||  | |||       |||||||| || || ||||||||||| |||||||| ||| | || || || ||||||||| |||| |||||||| |||||||| ||||| ||||| || || |
gtcggggtgtgatgtgtggaggggttgaacgccaagtggattgtactagcattggcattggtgttcggggtttaacgttgatgcctgtttggctctgcagGATCCCCAGACAGAGAACAATCCCTACCTGGGTTTCGTGTATACCTCGTTCCAGGAGAGGGCAACTTTCATTTCGCACGGTAACACTGCCCGTCATGCGA

upper sequence: EFJ09930 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S181_115V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------gtacgtagtctataaagttctaaacttctaaagttctctagagtt----ctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
                                                                                                                  ||   | |  |     ||       ||||  ||         |||         || |||| |       || |||  |    ||||| || |||||||||||||| |||||| |||| ||  | |||||||| || |||||| | || |||||||| ||||| || ||||| || || || || |
gtgagagtctgtaatcctactgagtccagtgaaaaatgtagcgtgatctgttttaccgcatgcttttgctgtcataccctgctgctagactcggggtatcgaagaggcctgtaagtgtattgattgatgggtagaggtgttctgtagggtatcgatgttggagtgtgagaattgactttgaatattatttggtgttgcagGACCCCCAAACCGAGAACAACCCTTACTTGGGTTTTGTTTACACGTCTTTTCAGGAGAGAGCAACTTTCATATCGCATGGTAACACTGCACGGCATGCGA

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|169115552|gb|FE518061.1|FE518061
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169095956|gb|FE497308.1|FE497308
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169048628|gb|FE454471.1|FE454471
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169053114|gb|FE463013.1|FE463013
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACNTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169082322|gb|FE490626.1|FE490626
EST:     GAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: GAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169053115|gb|FE463014.1|FE463014
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGNGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169048627|gb|FE454470.1|FE454470
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169095955|gb|FE497307.1|FE497307
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
EST: gi|169115553|gb|FE518062.1|FE518062
EST:     ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATG                         GATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC
genomic: ACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTC

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: 32 (upstream exon), 32 (downstream exon)
Score: 10

CAGGCACGGCGATCTCCTCAACAAGTATCTCTACTTGACCGGACGAGTGGACATGAAGAAGATCGAGCAAACGATCCAGTACCTGATTGGATCTGGCATGgtacgtagtc ... tttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaagttctctagagttctctcgagttgattgaagtgtttcttttttcaaccagGATCCACAAACCGAGAACAATCCTTACCTGGGGTTCATCTACACGTCCTTCCAGGAGCGGGCCACTTTCATCTCGCACGGCAACACCGCCCGCCACGCCA
                                      tttcttttttcaacc  CT-rich tract
                                      tttctttttt  TA-rich tract