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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcgagcttgccgcaagcatcgcattgctctctcttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA

Basic information

species Selaginella moellendorffii
transcript EFJ20024
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 2
--------gtaggcgagcttgccgcaagcatcgcat-tgctctctcttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
         | |    | |      ||  |  |  | ||  |  | ||| | ||| |  || |   || | ||| | || |||   |   ||    | ||||||||||| |||||||| || || ||| | ||||||||||| ||||| || ||||| |||||||||||  ||||| |  | || |||||||| ||||| |
ccttctaaattgattcgttattactaataagtgtgtgtgaccattgtttgagttctgttatggtggttgtagtaaaatt-gatatgttggttaatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTA

upper sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
-------gtaggcgagct--tgccgcaagcatcgcattgctctctcttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
         ||  ||  |  |  | |   ||      ||  |  | ||| | ||| |   | |   |    ||| | || |||   |   ||  | | ||||||||||| |||||||| || || ||  | ||||||||||| ||||| || ||||| |||||||||||  ||||| |  | || |||||||| ||||| |
taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaatt-gatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA

upper sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S14_33V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------gtaggcgagcttgccgc-aagcatcgcattgctctctct---tttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
                                            |   |   |    |  |||  | |  |||     | |   || | | |||     |   || |  | | |   | ||    |  |   || ||||| ||||| || ||||||||||| ||| | || ||||||||||| || ||||| ||||||||||||||  |||||||| | ||||| || || || || |
gtgcgggagggtgaattgaagtgggttagttgttttgttctttcaattggattgattgttaagtttggttttgtaaggtttgggttgagtccggttggggtttttataatcgtgccgggtttcggtgatcggttgcagGTGTATCCTGAGGGAACGCATTTTATGATTCCCTGGTTTGACAGACCTGTGATATACGATGTCCGTGCACGACCCAACATTGTCGAAAGCACATCAGGAA

upper sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaggcgagcttgcc-gcaagcatcgcattgctctct----------------cttttatttcggggatcgccctttttgtagagttcgattgatctt-----ttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
||  | |||   |   |   | || |||||| ||| |                  ||| |||  ||| | |    |||||  ||    |   ||| |      | ||||| ||||| ||||| || ||||||||||| ||| | || ||||| |||||||| ||||| || |||||||||||  |||| ||| | |||||||| || || || |
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttgga--ttttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA

upper sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S215_63V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------gtaggcgagcttgccgcaagcatcgcattgctctctcttttatttcggggatcgccctttttgtagag---ttcgattgatcttt-------tgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
                                                       | |    | ||    | ||   |   |||   | |   |   |  |    | |   | | || |  |   || ||| | | ||        || ||| ||||| |||||||| || |||||||| ||| | || ||||| |||||||| || |||||||||||||| ||  |||| ||  | || ||||| || || || |
gtacagtggtcgaaatcggtgctttttttttttttttttttttttttgttttttttcgcttggtttcagtctaggtccagtttgaatttttgctggctaggaatttgggtgtgtctggacggggttttgatggctgttaggaatggtggcttgcagGTTTATCCCGAGGGTACGCATTTCATGATTCCCTGGTTCGACAGGCCTGTCATCTACGATGTCCGAGCACGACCTAATATCGTTGAGAGCACCTCAGGAA

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|169034220|gb|FE445060.1|FE445060
EST:     CCGGGCATCGCGCCATCGTCTTCAATCGCCTCGTCGGGGTCAAGGACAAG                         GTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTG
genomic: CCGGGCATCGCGCCATCGTCTTCAATCGCCTCGTCGGGGTCAAGGACAAGgtaggcgagc ... tgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTG
EST: gi|169107474|gb|FE504196.1|FE504196
EST:     CCGGGCATCGCGCCATCGTCTTCAATCGCCTCGTCGGGGTCAAGGACAAG                         GTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTG
genomic: CCGGGCATCGCGCCATCGTCTTCAATCGCCTCGTCGGGGTCAAGGACAAGgtaggcgagc ... tgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
                                  gattgat  putative branch site (score: 4)
                                        tcttttgccttcc  CT-rich tract
                    tttttgta  TA-rich tract