Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcgtttcctctttgtttttatctttgtaggaaacattatttttgtttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTGACTATGACAAAAGATTGTCTCACGCTGTTACTGCTCATCCCAAAGTTGA

Basic information

species Selaginella moellendorffii
transcript EFJ09546
intron # 6
splice site 3'
intron type U2

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|169115410|gb|FE516151.1|FE516151
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169029569|gb|FE438930.1|FE438930
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|70669547|gb|DN838124.1|DN838124
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169079267|gb|FE490156.1|FE490156
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169075081|gb|FE481454.1|FE481454
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169088397|gb|FE495443.1|FE495443
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169078772|gb|FE489622.1|FE489622
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169060192|gb|FE467554.1|FE467554
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169041742|gb|FE449300.1|FE449300
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCT
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCT
EST: gi|169052819|gb|FE461197.1|FE461197
EST:     ATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: ATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169106155|gb|FE507947.1|FE507947
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169099588|gb|FE502621.1|FE502621
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169054031|gb|FE461330.1|FE461330
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169088169|gb|FE493395.1|FE493395
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|70670735|gb|DN839312.1|DN839312
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169045092|gb|FE450936.1|FE450936
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
EST: gi|169078721|gb|FE487556.1|FE487556
EST:     GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT                         ATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG
genomic: GGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTG

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: 34 (upstream exon), 35 (downstream exon)
Score: 27

CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCATgtaagctcgt ... tttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTGACTATGACAAAAGATTGTCTCACGCTGTTACTGCTCATCCCAAAGTTGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtttcctctttgtttttatctttgtaggaaacattatttttgtttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTGACTATGACAAAAGATTGTCTCACGCTGTTACTGCTCATCCCAAAGTTGA
                                    ttatttttgttttt  CT-rich tract
                               aaacattatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcgtttcctctttgtttttatctttgtaggaaacattatttttgtttttgtcagATGCTATTCGAATGCTCGAAGATGGGAACCTTGAGACAATTGGCGTGCTTGACTATGACAAAAGATTGTCTCACGCTGTTACTGCTCATCCCAAAGTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT