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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgaccaaagaggtgctctgtttctgtggttcatacttgcaaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ24514
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24514 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA14G06630.1 (Glycine max), 3'ss of exon 3
------------------------------------------gttcgaccaaagaggtgctctgtttctgt--ggttcatacttg----caaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG
                                              |  |||     |  | | ||  |||   ||| || |||     |    || ||||| ||||||||||| |||||||| |||||||| ||||| || ||| |  |  | ||||||||||| || |||||||| || ||||| || || || || |
tacagattttttataagagttctgtttttaaaatcaaggaaaaacaggtcaagattattttgttttcatgtcatgtttatgcttagtttctgtatttcagGTGCTCAACATTCCTACCAAGATTAACAAGGGTACTGTTGAAATCATTACCCCTGTGGAGCTCATTAAGAAGGGAGACAAGGTTGGATCTTCTGAAGCTG

upper sequence: EFJ24514 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S38_196V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------gttcgaccaaagaggtgctct---------gtttctgtggttcatacttgcaaact-tccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG
                                                                                                     |   |   | ||   ||| |         |||||||  |   | | |    |||| ||||||| || ||||||||||||||||| |||||||| |||||||||||  || |  | || |||||  || | ||||| || || || || || || ||||| |
gtaaggtcttcggtatatggtatgttctatgaatgagattccagtcagtcaatttagcttatcgcagtgggcaagtgtcctttttctgatgtcgttctttatggcagttatgaaacgctgttaactgaaggtttctgacgaatagaatgctgaactctccagGTCCTTAACATTCCCACCAAGATTAACAAGGGTACTGTCGAGATTATCGCCCCTGTCGAGCTTGTCCACAAGGGTGACAAGGTCGGATCGTCCGAGGCTG
















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|169059624|gb|FE468858.1|FE468858
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169102451|gb|FE503893.1|FE503893
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169059623|gb|FE468857.1|FE468857
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169078881|gb|FE489653.1|FE489653
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169060805|gb|FE469220.1|FE469220
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169109252|gb|FE512819.1|FE512819
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169040256|gb|FE448971.1|FE448971
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169114856|gb|FE516117.1|FE516117
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169103625|gb|FE506822.1|FE506822
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169035321|gb|FE443765.1|FE443765
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169053545|gb|FE463314.1|FE463314
EST:     GAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: GAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169109253|gb|FE512820.1|FE512820
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169053687|gb|FE461506.1|FE461506
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169045016|gb|FE452758.1|FE452758
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169103624|gb|FE506821.1|FE506821
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169114855|gb|FE516116.1|FE516116
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169078880|gb|FE489652.1|FE489652
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169040255|gb|FE448970.1|FE448970
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169053546|gb|FE463315.1|FE463315
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169060804|gb|FE469219.1|FE469219
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169053686|gb|FE461505.1|FE461505
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169035320|gb|FE443764.1|FE443764
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169045002|gb|FE452757.1|FE452757
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169102450|gb|FE503892.1|FE503892
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
EST: gi|169074146|gb|FE481871.1|FE481871
EST:     TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAG                         GTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG
genomic: TTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCG

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: 64

GTTGGAGCGCCTGCTCGTGTCGGACTTGTTGCCCCGATCGACGTGACCATTCCTCCTGGAAGCACTGGGCTTGATCCCTCGCAGACATCTTTCTTCCAGgttcgaccaa ... aaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgaccaaagaggtgctctgtttctgtggttcatacttgcaaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG
                                                  cttcc  CT-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgaccaaagaggtgctctgtttctgtggttcatacttgcaaacttccagGTTCTCAACATTCCCACCAAGATCAACAAGGGAACTGTCGAGATCGTCTCGTCCGTGGAGCTCATCAAAAAGGGAGAGAAAGTTGGCTCCTCGGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC