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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcgacacttgactgcttacacctctttgttcttgctcaatatctcgcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAAAGCCATCATCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTA

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 21
lower sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 21
--------------------------gtaagcatcgacacttgactgcttacacctctttgttcttgctcaatatctcgcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAAAGCCATCATCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTA
                           | |     || |  || |  |  ||  |  ||    |||| ||  | ||  | ||  | |||   ||  | |  ||| ||||  ||||||| || |||||| | ||||||||  ||| |||||||||||| ||||||||| | ||||||  | | || || 
gtgagtgtcgatctcttagcacccatttcactcgtgaaaaatgccgccgaactgcatttcaaccttgttctct-tcctgtttcctcagGATGGCACTTGGGGGCCTTGTAACCGTTCTCCACGCGTGCCTTGATATGAAGTCCACCATCCTAGGGAAATACCACTACATCCTCTACATTATTGTCCTG
















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|169064751|gb|FE476097.1|FE476097
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169025374|gb|FE435988.1|FE435988
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169088930|gb|FE494442.1|FE494442
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169088931|gb|FE494443.1|FE494443
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169019957|gb|FE431022.1|FE431022
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169080935|gb|FE486104.1|FE486104
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169030421|gb|FE438677.1|FE438677
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169116305|gb|FE517252.1|FE517252
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169066440|gb|FE474663.1|FE474663
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169028508|gb|FE439923.1|FE439923
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169097980|gb|FE498777.1|FE498777
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169064752|gb|FE476098.1|FE476098
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169059060|gb|FE468205.1|FE468205
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169116306|gb|FE517253.1|FE517253
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169097109|gb|FE498955.1|FE498955
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169064768|gb|FE473735.1|FE473735
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCTCCGGCATTATTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
EST: gi|169025373|gb|FE435987.1|FE435987
EST:     GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGAC                         GCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA
genomic: GGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAA

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: 33 (upstream exon), 14 (downstream exon)
Score: 7

GTTCGGATCGCCCAGGGACTTGTACACATGGGAAAGGGACTAATCACTTTAAATCCTTACCATTCTGATCGTTTCTTGCTCTCGACgtaagcatcg ... gcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAAAGCCATCATCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgacacttgactgcttacacctctttgttcttgctcaatatctcgcttgtttagGCCTGCCATCGCCGGCATTGTTGCCGTTCTTCATGCGTGCTTGGATATGAAAGCCATCATCCTAGGGAAGTACCACTACGTTCTCTACTATCTCGTTCTA
            tgcttac  putative branch site (score: 7)
                                         tctcgctt  putative PPT
                                   tcaatat  TA-rich tract