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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGCTCAAGTTCCAGAGAAACTTGAGATCCGTGGCCGAGGAACGTGCTGGGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctagactcttccgattcttccagctctaaaactgtggagaactttggattccag

Basic information

species Selaginella moellendorffii
transcript EFJ27946
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27946 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 5'ss of exon 3
CCAGCTCAAGTTCCAGAGAAACTTGAGATCCGTGGCCGAGGAACGTGCTGGGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctagactcttccgattcttccagctctaaaactgtggagaactttggattccag-----------------------------------------
 ||||| ||||||||| | |||||| |||| || || ||||| || || ||  | ||||| ||    ||  | ||||||||||| ||||||||||||||||||   | | | |  |  |||   |   | | |   | |    | ||    || |   |                                          
ACAGCTTAAGTTCCAGCGTAACTTGCGATCAGTAGCTGAGGAGCGGGCAGGAAGGAAGCTTGGAGGCCTTAGGGTCCTCAACTCTTACTGGATCAACCAGgtatgtccatatttatg-gatctgtttggtttttgtaataaacacaatcgagggtctgatcgttttgaatactgccaattaggtgcgagttgctaattaat
















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|169047288|gb|FE456537.1|FE456537
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169058518|gb|FE464244.1|FE464244
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169058894|gb|FE468728.1|FE468728
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169070557|gb|FE479834.1|FE479834
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169063696|gb|FE471802.1|FE471802
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169101168|gb|FE501925.1|FE501925
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169109682|gb|FE511754.1|FE511754
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169101169|gb|FE501926.1|FE501926
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169109683|gb|FE511755.1|FE511755
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169073901|gb|FE482991.1|FE482991
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169021073|gb|FE430682.1|FE430682
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169038352|gb|FE443986.1|FE443986
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169038351|gb|FE443985.1|FE443985
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169058895|gb|FE468729.1|FE468729
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169021074|gb|FE430683.1|FE430683
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|70670086|gb|DN838663.1|DN838663
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169096233|gb|FE497819.1|FE497819
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169096234|gb|FE497820.1|FE497820
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169047289|gb|FE456538.1|FE456538
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169073900|gb|FE482990.1|FE482990
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169058517|gb|FE464243.1|FE464243
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
EST: gi|169070556|gb|FE479833.1|FE479833
EST:     GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAG                         GACTCAACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC
genomic: GGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACC

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: 34

CCAGCTCAAGTTCCAGAGAAACTTGAGATCCGTGGCCGAGGAACGTGCTGGGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctag ... tggattccagGACTCGACTTACAAGTACTTTGAGATCATCCTCATCGACCCAATGCACACCGCGATTCGCAAGGACCCAAGGATCAACTGGATCTGCCAGCCGGTTCACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGCTCAAGTTCCAGAGAAACTTGAGATCCGTGGCCGAGGAACGTGCTGGGCGCAAGCTGGGCAATCTCCGCGTCCTCAACTCCTACTGGATCAACCAGgtactgctagactcttccgattcttccagctctaaaactgtggagaactttggattccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG