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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCAGGAACTCCAACTCGGTGCGCGAGTACCTGGAGAAGAACTACACCGAGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaagagttttggattgcgcttctctcggatctgtctaacttttggaactcgtgggtctatag

Basic information

species Selaginella moellendorffii
transcript EFJ34636
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G042604_T01 (Zea mays), 5'ss of exon 2
GGGCAGGAACTCCAACTCGGTGCGCGAGTACCTGGAGAAGAACTACACCGAGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaagagttttggattg-cgcttctctcggatctgtctaacttttggaactcg---tgggtctatag----------------------------
||| ||||||||||||||  |||| |||| |||||||||||||||||  ||||| || |||| ||| ||  | || || ||| |||| || || || ||||||       | |  |  ||    ||   | |    |   |  || || || |||  |   ||   |||  |                            
GGGAAGGAACTCCAACTCTATGCGTGAGTTCCTGGAGAAGAACTACAAGGAGACCTCCGGCAAGGAGACCATCAAACTTGCTATCCGTGCACTTCTAGAGgtatatcgtaattcataaataaatgcactttttaatttcctgcaatttatgcaacatgctatgaacctaatgcagtctaggttttgctgatattttggtt
















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|169053862|gb|FE460953.1|FE460953
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169067023|gb|FE474440.1|FE474440
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169073950|gb|FE483430.1|FE483430
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169049283|gb|FE459559.1|FE459559
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169067024|gb|FE474441.1|FE474441
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169051265|gb|FE457615.1|FE457615
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169092978|gb|FE495272.1|FE495272
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169092979|gb|FE495273.1|FE495273
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169051264|gb|FE457614.1|FE457614
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169049284|gb|FE459560.1|FE459560
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169053861|gb|FE460952.1|FE460952
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169073951|gb|FE483431.1|FE483431
EST:     AGACGTCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
EST: gi|169071075|gb|FE480703.1|FE480703
EST:     AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAG                         GTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA
genomic: AGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAA

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: 32 (upstream exon), 33 (downstream exon)
Score: 20

GGGCAGGAACTCCAACTCGGTGCGCGAGTACCTGGAGAAGAACTACACCGAGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaag ... gggtctatagGTTGTGGAGAGCGGTGGCAAGAACATCGAGATCGCTGTGATGACCAGACAAGGACTGAAATTGCTGGAGGAGCCCGAGATCGAAGAGATTGTTAACGGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCAGGAACTCCAACTCGGTGCGCGAGTACCTGGAGAAGAACTACACCGAGACATCGGGCATGGACACGGTGAAGCTGGCTGTCCGAGCTCTCCTGGAGgtaagcaaagagttttggattgcgcttctctcggatctgtctaacttttggaactcgtgggtctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG