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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttagattcacgttagctagaaatgagactaattttccgcttacag

Basic information

species Selaginella moellendorffii
transcript EFJ11831
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11831 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: LOC_Os10g41590.2 (Oryza sativa), 5'ss of exon 15
ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttagattcacgttagctagaaatgagactaattttccgcttacag---------------------------------------------------------------------------------------------------------------------------------------
|| || || ||||||||||||||||||||||| ||||| ||    ||| | || ||| |  | || || |||||||  || | |||||| | ||||||   | | |             |   | |   | |    |                                                                                                                                       
ACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAGgtat-ttagatatccatcaatcttgttgcttgcctttgtagagttcctggtagtctgtagcaccttacacggctagtaggtgcagggatttatagactgttctagattctagaaccaaagctaatctgctcttttttccccaatcacaagttggttcctgtcctaacatggttctcatctaacag

upper sequence: EFJ11831 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GRMZM2G341271_T02 (Zea mays), 5'ss of exon 16
ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGg--tttgttagat-tcacgttagctagaaatgagactaattttccg-cttacag----------------------------------------------
||  | || ||||||||||||||||||||||| ||||| ||    ||| | || ||| |  | || || ||||| |  || | |||||  ||| || | | || | ||  | |       | | ||  | |   || | |                                               
ACAGTTGGTCAAGCATATGAAGACATGCAAACGCAAAATCAGCATCTTCTTCAACAGCTTACTGATAGAGATGACTTTAACATAAAGgtatttatttgttctctccttttccactttcacgtcaaagctgcaaactcataacatacagattggaattggagatacatgcccggggtttttatgccaa

upper sequence: EFJ11831 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GRMZM2G341271_T06 (Zea mays), 5'ss of exon 1
-------------ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGg--tttgttagat-tcacgttagctagaaatgagactaattttccg-cttacag----------------------------------------------
             ||  | || ||||||||||||||||||||||| ||||| ||    ||| | || ||| |  | || || ||||| |  || | |||||  ||| || | | || | ||  | |       | | ||  | |   || | |                                               
ATTTGCAATACAGACAGTTGGTCAAGCATATGAAGACATGCAAACGCAAAATCAGCATCTTCTTCAACAGCTTACTGATAGAGATGACTTTAACATAAAGgtatttatttgttctctccttttccactttcacgtcaaagctgcaaactcataacatacagattggaattggagatacatgcccggggtttttatgccaa

upper sequence: EFJ11831 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GLYMA01G13430.1 (Glycine max), 5'ss of exon 10
ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttagattcacgttagctagaaatg---agactaattttccgcttacag-----------------------------------------------
| ||| || ||||||||||| |||||||||||||||||||||   || |||||||||||  | ||||| |||||||| ||||  |||||   ||   || |  || | |  |  |    ||  || |||     | |                                                  
AGTATTGGACAAGCATATGACGACATGCAAACTCAAAACCAACATCTGTTGCAGCAGATTACTGAAAGAGATGATTATAATATTAAGgtaatttgtcttgaaattggttgcacctttatagtttactttgaaagtgatgataatttatttctacagtacatataaacaagaccctttgtatttctca

upper sequence: EFJ11831 (Selaginella moellendorffii), 5'ss of exon 15
lower sequence: GLYMA11G26740.1 (Glycine max), 5'ss of exon 3
ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttagattcacgttagctagaaatgagactaattttccgcttacag----------------------------------------------------
| ||| || || |||||||| ||||||||||||||||| |||   || |||||||||||  | ||||| |||||||||||||  |||||   ||   || |  || | |  |  |     || |||| |  ||| ||                                                    
AGTATTGGACAGGCATATGACGACATGCAAACTCAAAATCAACATCTGTTGCAGCAGATTACTGAAAGAGATGATTACAATATTAAGgtaatttgtcttgaaattggttgcaccttta--tagttttacttttaaagttatgatgatttatttctatggtctttgccatctacatataaaacaagactc

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|169115605|gb|FE517815.1|FE517815
EST:     ACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAG                         CTTGTGGCGGAAAGCTTGAAAGCAAAACAGTTGCAGACCTCTCTTGTTGCT
genomic: ACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
EST: gi|169031779|gb|FE440609.1|FE440609
EST:     AGGCTTTTCCAGCAGATATCCGAAAGGGATGATTACAATACAAAG                         CTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
genomic: AGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
EST: gi|169115604|gb|FE517814.1|FE517814
EST:     ACCAAAGGTTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAG                         CTTGTGGCGGAAAGCTTGAAAGCAAAACAGTTGCAGACCTCTCTTGTTGCT
genomic: ACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
EST: gi|169067312|gb|FE473897.1|FE473897
EST:     TTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAG                         CTTGTGGCGGAAAGCTTGAAAGCAAAACAGTTGCAGACCTCTCTTGTTGCT
genomic: TTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
EST: gi|169030807|gb|FE439791.1|FE439791
EST:     AAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAG                         CTTGTGGCGGAAAGC-TGAAAAGCAAAACAGTTGCAGACCTCTCTTGTTGC
genomic: AAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTG-AAAGCGAAACAGTTGCAGACCTCTCTTGTTGC
EST: gi|169045077|gb|FE452793.1|FE452793
EST:     CCGAAAGGGATGATT-CAATACAAAG                         CTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT
genomic: CCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCT

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), 28 (downstream exon)
Score: 13

ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttaga ... ccgcttacagCTTGTGGCGGAAAGCTTGAAAGCGAAACAGTTGCAGACCTCTCTTGTTGCTGAGAAACAGTCGATATCTGGGAAGATGCAGCTTGCAACGTCTGCAGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAGgtttgttagattcacgttagctagaaatgagactaattttccgcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT