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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatttggcagattccataactgatctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

Basic information

species Selaginella moellendorffii
transcript EFJ28889
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------------------------------------------------gtaggatttggcagattccata----actgatctaatctacat-tgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                                                          |   |||||    |||   |    | | | |||||   ||| | |  | |     ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | |||||||||||| || || || ||||| |||||||| |||||||
gtcagtatccttgtgtactgtttgtgttttctagactttgcacctggctgtttgagaaaacaaaataaatatatttattgaagcattaacaaagtttggtttgttctgcattgaagtaagctaattggcatgtattttatactttcagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTTTCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGGTGTGTCAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 10
--------------------------------------------------------------------------------------------------gtaggatttggcagattccataactgatctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                                                                    |   |||||    |||   |  |||  ||| |||  | |    | ||   ||||||||||| |||||||||||||| |||||||||||    |||||||| || || | ||| |||||||| || ||||| |||||||||||||| |||||||
gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgca-ttgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G112149_T03 (Zea mays), 3'ss of exon 10
------------------------------------------------------------------------------------------------------gtaggatttggc--agattccataactgat--ctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                                                                       ||   |||| |  || |   |||  |  |   | || || ||     | | |   |||||||| ||||||||||||||||||||||||||  |    |||||||| ||||| | |||||||||||| || ||||| ||||| || ||||| |||||||
gtgagcatttcagtgtaatgctttgtttattgtagactacctgcattagctttttttttgtctggatcactaaaaataacaagttcttttaggatattgatattaatgtttgtcgaaggtgaaatatttacttatttatgtaaatgcctatgtatttacagAGAAATGACATGGTTGAGTACTTCGGTGAGCAATTATCTGGTTTTGCGTTCACTGCCAACGGATGGGTGCAATCCTATGGATCACGCTGTGTGAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G165747_T02 (Zea mays), 3'ss of exon 10
-------------------------------------------------------------------------------------------------------gtaggatttggcagattccataactgatctaatctacat---tgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                                                                        ||   ||||    |    | |  |   || || ||  |   || |  | ||   |||||||| ||||||||||||||||||||||||||  |    |||||||| ||||| | |||||||||||| || || || ||||| || ||||| |||||||
gtgagcattttagtgtcatggtttgtttattgtagactaactgcattagcttttttttttctatggatcacttaaattagcaagatcttttaggatattgataatattgtttgctgaagatgaaacatttacttatttatgtcaatgcctatgttttacagAGAAATGACATGGTTGAGTACTTCGGTGAGCAATTATCTGGTTTTGCATTCACTGCCAACGGATGGGTGCAATCTTATGGATCACGTTGTGTGAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
-----------------------------------------gtaggatttggcag-attccataactg-------atctaatctac---attgtcct-ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                           | |||    |   || |||| | ||       || ||||  ||   |||| ||| | |||  ||||||||||| ||||||||||||||||||||||||||    |||||||| ||||| | ||| || ||||| ||||| || || ||  |||| || ||||| |
gtcagtgctcttgaatccattctgctggtttttgatgtctaagaagataaacccccataccatgagtgtagtcgcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA19G29180.2 (Glycine max), 3'ss of exon 9
-----------------------------------------gtaggatttggcagattccataactg---atctaatctacattgt---cctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                          |  ||||  || ||||| | || ||    || ||   |   |||   | |||  |  |||||||| || |||||||||||||||||||||||  ||  ||| ||||| ||||| || || || ||||| || ||||| || ||||| ||||| |||||||
tctgaagagcaactactcttgccagattttcttcccttttttttagatt--gctgattctaaaattgcacctccaactaattgtgtatgcatttcactgcagAGAAATGATATGGTTGAGTACTTCGGTGAGCAATTGTCAGGCTTTGCCTTCACTGTTAATGGGTGGGTGCAATCCTATGGTTCCCGTTGTGTGAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GLYMA16G04240.3 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------------------------------------------gtaggatttggcagattccataactga------tctaatc---tacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                                                                         ||  ||||  || ||||||| || ||       || ||     |  ||   | |||  |  |||||||| || |||||||||||||||||||| ||  ||  ||| ||||| |||||||| || || ||||| || ||||| || ||||| || || |||||||
gtccgctctcatttcataacatgactaaatattagtcttttgaattgaagatagcttctttctttctgaagagcaactactctttgcatattttctttccttattgttagatt--gctgattccaaaattgcagcacctccaactaattgtatatgcatttcactgcagAGAAATGATATGGTTGAGTACTTCGGTGAACAATTGTCAGGCTTTGCCTTCACCGTTAATGGGTGGGTGCAATCCTATGGTTCCCGTTGCGTGAAGCCAC

upper sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------gtaggatttggcagattccataact--gatctaatcta-cattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                                                           | |||   |   | ||  |||| |    | |||| |  || || | |  |    |||||||| ||||||||||||||||| || |||||  |   ||||||||| ||||| ||||| || ||||| || || || || ||||| ||||| |||||||
gtgatttctcttcctaattatctaaaattaattcaatgcttcatggctatattttgttatgggaaa-gaaggtttaaataatttcattgtaatttgtcaatggcttgatgatgcagAGAAATGACATGGTTGAGTACTTTGGGGAGCAATTATCAGGTTTTGCCTTCACTGTCAATGGGTGGGTCCAATCTTATGGGTCCCGTTGTGTCAAGCCAC

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|169057672|gb|FE463723.1|FE463723
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
EST: gi|169101347|gb|FE502516.1|FE502516
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
EST: gi|169053883|gb|FE460974.1|FE460974
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
EST: gi|169032658|gb|FE436931.1|FE436931
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTTCG-TGAGCAGCTGCAAGGTTTTG
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTT-CGGTGAGCAGCTGCAAGGTTTTG
EST: gi|169060120|gb|FE468106.1|FE468106
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
EST: gi|169061439|gb|FE469538.1|FE469538
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAA
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAA
EST: gi|169109744|gb|FE511815.1|FE511815
EST:     AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAG                         AGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC
genomic: AGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTC

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: 217

CGAGGAAGAGTACGTGACGGCCATCAAATCTGAAATCGCCAGCGTTGTGAAGCTCCAGGAGGAGCTTGATATTGACGTCCTCGTCCACGGAGAACCCGAGgtaggatttg ... ttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggatttggcagattccataactgatctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC
                          atctaat  putative branch site (score: 217)
                                      ttgtcctttttcgcc  putative PPT
                          atctaat  TA-rich tract