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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatttttctttcttttttggccttggtgctaagagttctctactttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ34304
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34304 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S136_175V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------gtttgatttt---tctttcttttttggccttggtgctaagagttctctactttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG
                                                                           | ||   | |   ||  | | | |   |    || ||     | || |   || | ||||| |||||||| || || |||||||||||||||   || |||||||||||||||
gtccgtacttgcggttgaatgtgtatcgtggaatgacagaattgtgggtgtatgttatttccccatctattataagcttaggtgtaggtcaatttgtctcaactgacgtactttctatcctgtgtatttttagGGCTTGCTATGGAGTGCTGAGGTTCATCATGGAGAGCGGTGCCAAGGGTTGTGAG

upper sequence: EFJ34304 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------gtttgatttttcttt-cttttttggcc----ttggtgctaagagttct-----ctac--tttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG
                                                                     || ||| || | ||  |    ||||        | | |||  ||||||     || |  ||| | ||||| |||||||| || || |||||||||||||||   || |||||||||||||||
gtttgtgcttctacacaaaatatacttttaaatggcaattaaatttattcaattaaatggtaattgaatgtatgaattgttttagccaaattggaaaaaagggatactataagttcttgaacctgcggttttttagGGCTTGCTATGGAGTGCTGAGGTTCATCATGGAGAGCGGTGCCAAGGGTTGTGAG
















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|169072227|gb|FE479359.1|FE479359
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169038060|gb|FE446658.1|FE446658
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169043108|gb|FE454022.1|FE454022
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|70671143|gb|DN839720.1|DN839720
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAAGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169038061|gb|FE446659.1|FE446659
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169103365|gb|FE507342.1|FE507342
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169044789|gb|FE454104.1|FE454104
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169073958|gb|FE481670.1|FE481670
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169067196|gb|FE474964.1|FE474964
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169034020|gb|FE444210.1|FE444210
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169073959|gb|FE481671.1|FE481671
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169034021|gb|FE444211.1|FE444211
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169055910|gb|FE465111.1|FE465111
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169055911|gb|FE465112.1|FE465112
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
EST: gi|169043107|gb|FE454021.1|FE454021
EST:     CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAG                         GGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG
genomic: CAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTG

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: 102

TGGAGCTGTATGCCGAGAAGGTGAACAACCGTGGCCTCTGCGCCATCGCTCAAGCCGAGTCTTTGCGATACAAGCTCCTGGGAGGACTGGCCGTCCGAAGgtttgatttt ... actttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatttttctttcttttttggccttggtgctaagagttctctactttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG
                                       ttctctactttgtc  CT-rich tract
     atttttctttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatttttctttcttttttggccttggtgctaagagttctctactttgtcagGGCCTGCTATGGTGTTCTCAGGTTCATCATGGAGTCTGGAGCCAAGGGTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA