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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagacttcttcctctctttcctcagtcttctgatgactcgaatttgttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA

Basic information

species Selaginella moellendorffii
transcript EFJ27687
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------------gtcagacttcttcctctctttcctca-gtcttctgatgactcgaatttgttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA
                                                                                     |||  |         | |  | | || |  | ||    | |  ||||| | |||||||  |||| ||| | ||| | ||  |  | || |||||||||||||| ||||| ||||||||||| ||||| || ||||| || ||||| || |||
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttat-ttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA

upper sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------gtcagacttcttcctctctttcctcagtcttctgatgactcgaatttgttttgtt-cagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA
                                                                      |   |||||      || || ||        |  | | | |  ||| | | | | ||||| ||||| ||| | ||  |||| ||||| |||||||| || ||||||||||||||||| ||||| ||||| || ||||| || || || || || 
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
















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|169067517|gb|FE475259.1|FE475259
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169067518|gb|FE475260.1|FE475260
EST:     CAGAGTGATGACACCTGCTGAGGAGTCAATCCCACA-GATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGANCA-TACTAA
genomic: CAGAGTGATGACACCTGCTGAGGAGTCAATCC-ACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGA-CAATACTAA
EST: gi|169082641|gb|FE486200.1|FE486200
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169071278|gb|FE478410.1|FE478410
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAG-TCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169037362|gb|FE443308.1|FE443308
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169071277|gb|FE478409.1|FE478409
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169112908|gb|FE514660.1|FE514660
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTTAAATCCGAAAGGTCGCATTTG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACT-AAATCCGAAAGGTCGCATTTG
EST: gi|169082642|gb|FE486201.1|FE486201
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169044046|gb|FE451632.1|FE451632
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169102323|gb|FE506547.1|FE506547
EST:     GAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
EST: gi|169064650|gb|FE471381.1|FE471381
EST:     GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAG                         ACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG
genomic: GCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGG

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), 35 (downstream exon)
Score: 53

GTGGGGCAATGTGGAATTTCCAGTTCCATTTGGCAGAGTGATGACACCTGCTGAGGAGTCAATCCACAAGATGGATGAAAAGgtcagacttc ... ttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacttcttcctctctttcctcagtcttctgatgactcgaatttgttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA
                          ttctgat  putative branch site (score: 53)
                                         tttgtttt  putative PPT
                                       aatttgtttt  TA-rich tract