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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG

Basic information

species Selaginella moellendorffii
transcript EFJ26297
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 14
---------------------------------------------gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG
                                               |||||   || |     |    ||  |     | || ||  | ||||| ||||||||||| || ||| | || |||||||||||||| ||  |||| || || |||||||||||||||||  | |||||||||
gtaatattcgtcatctaatttgtgtggggtggggtgggtacgtcgagtttgggtgtgtcat---caggcttaactaaggtaatgctg-tgtgtttccagGTGAATGCTATTCAGATGAAGGAGACGGTTGAAGAAAACACAAGCACAACTGAGAGAGTATTCCAGGACAGACAGTATCAG

upper sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 14
-------------------gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG
                     ||||||  || | |  |  |    ||  |  ||  |  |  |  | || ||||| |||||||| ||  | ||||||||||| ||||| ||  | || ||||| |||||||| |||||||||||||||||||||
gtaatgtatgtacacatacactttggatttgac-atggtcattaagcttgaact-gttgttttgcgcttccagGTAAATGCAATTCAAATGAAAGAGACGGTAGAAGAAAACACGAGCACCACTGAGAGAGTGTTCCAGGATCGGCAGTATCAG

upper sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 2
-------------------gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG
                     ||||||  ||    | | |  ||    | |     |  |  |    || ||||| |||||||| ||  | || |||||||| ||||| ||  | || ||||| |||||||| |||||||||||||||||||||
gtaatatatgtacacatacactttggatctgat--atg-gtcatcaatctttactgttgttatgcacttccagGTAAATGCAATTCAAATGAAGGAGACGGTAGAAGAAAACACGAGCACCACTGAGAGAGTGTTCCAGGATCGGCAGTATCAG

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|169052725|gb|FE461155.1|FE461155
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169083877|gb|FE492789.1|FE492789
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169077256|gb|FE485142.1|FE485142
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTGAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169078485|gb|FE488360.1|FE488360
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169053211|gb|FE462486.1|FE462486
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTGAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169039037|gb|FE450443.1|FE450443
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCANAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169078955|gb|FE487634.1|FE487634
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169094797|gb|FE492948.1|FE492948
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTGAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169094958|gb|FE493005.1|FE493005
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTGAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
EST: gi|169039036|gb|FE450442.1|FE450442
EST:     ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAG                         GTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA
genomic: ACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACA

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: 27

CAACCCAAAGGGAGAGAGGTGGAGGACGACGACGTGTTTACGTTCAATGAGGACTTCACGGCTCCTTTGTTCCGGATCAAGgttttggaca ... ttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG
            gcctaac  putative branch site (score: 27)
                         ttgcccgtcctcatcc  putative PPT
                                            tttgtttt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttggacatgcctaacgcgaaattgcccgtcctcatcctcctttgttttcagGTGAATGCAATACAGCTCAAAGAGACGGTTGAAGAGAATGCAAGTACCACAGAGAGAGTATTCCAGGATCGGCAGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA