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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttccctctgatctctagacctctagatttctagctcctgattccgaaatctctgtccag

Basic information

species Selaginella moellendorffii
transcript EFJ34636
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os08g43540.1 (Oryza sativa), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttccc--tctgatctctagacctctagatttctagctcctgattccgaaatctctgtccag-----
||||||| || |||||||||||||||||||||||||||||||| |||||  |||| |||||||| ||||||||||||||| |||||||||||||| | ||||   |    |   | |  | ||   | ||      |||  | |  |  || ||  || |   | |      
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCGTCGTCCTCGGCGTCGAGAAGAAATCCACCCCCAAGCTCCAGGACTCCAGgtaaatccttcaacccgccccctccccttcgccggatctcacccgcggatc-gatctcccccccaaatccag

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-----tcgtttccctctgatctct--------agacctc--tagatttctagctcctgattccgaaatctctgtccag
||||||| || |||||||||||||||||||||||||||||| | |||||  |||| |||||||| |||||||| |||||| |||||||||||||| | ||||     ||   |||    || ||||        | ||| |  ||||| ||      | | |   | | ||  |   |||
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G138128_T01 (Zea mays), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt----------tcgtt--tccctctgatct-----ctagacctctagatttctagctc------------ctgattccgaaatc---tctgtccag
||||||| || |||||||||||||||||||||||||||||||| |||||  |||| ||||| ||||||||||| || ||| |||||||||||||| | ||||           |||   ||||   ||||      | ||| |||  |||| |   |||            ||||  ||||| ||   |||  ||||
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACGGACACCGTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaaactaatatctctgaccccgaattcatgtctccccag

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G042604_T01 (Zea mays), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-------tcgtttccctctgatctctagacct---ctagatttctagctcctgattccgaa-----atctctgtccag-----------------
||||||| || ||||||||||||||||| |||||||||||||| |||||  |||| |||||||| |||||||| |||||  |||||||||||||| | ||||        | |    | ||  | ||||  |     | |||| ||  | ||||     | ||     ||||||| || |                 
AGGCCGTCCGCAAGGGCAACGCCGCCGTGGGCGTCCGCGGCACGGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACACCCAAGCTCCAGGACTCCAGgtagcaaacccctccgtccctcctttctatcctccgaccagatctcgcgatcctcgcctcaaactactatctctgacccgagtttccgtctccctag

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G050467_T01 (Zea mays), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgt----------------ttccctctgatct-ctagacctctagatttctagctcctgatt-ccgaaatctctgtccag-------------
||||||| || |||||||||||||| ||||||||||||||    |||||  |||| |||||||| |||||||| |||||| |||||||||||||| | ||||  ||                 ||||||  |||  | ||| |||| ||   |  || ||   |  || |||||     |||              
AGGCCGTCCGCAAGGGCAACGCCGCTGTCGGCGTCCGCGGTGTCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtcggtccgtcggtacctccccctccctcccatccaccagatctcttgaccccgggcgccgcctcacccaaatcctcccccaaaaaatctccgcag

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G05190.1 (Glycine max), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-tcgtttccctc-----tgatctctagacctctagatttctag--ctcctgattccgaaatctctgtccag---------------------------
| ||||| || |||||||||||||||||||||||||||||||| ||||   |||| |||||||| |||||||||||||||||||||||||| ||| | ||||  |  | | ||      |   | |    ||| |   ||  |||   |  | ||    |||| |  ||   |                           
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAACGTCGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAGCTCCAAGACTCCAGgtaccactactcttatcaattcccccctttcctttcccttattaggttttttaatcggcaaatgttagttttgttagcagagaggattttccctcttccc

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA16G23580.1 (Glycine max), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt--------tcgtttccctctgatctctagacctctagatttctagctcct--gattccgaaatctctgtccag-------------------------
| ||||| || |||||||||||||||||||||||||||||||| ||||   | || |||||||| |||||||||||||||||||| ||||| ||| | ||||        || ||||  |   ||  |      |  ||||  ||  | |||  |||| | |    |    | ||                         
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAATGTTGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAACTCCAAGACTCCAGgtactactactcttttcaattcaattccctccgtttcagatccctttccccttcgattactagggattaaccaagaaaactacgtgttataaggagaagg

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-tcgtttccctct------------gatctctagacc---tctagatttctagctcctgattccgaaatctctgtccag-------------------
| ||||| |||||||| |||||||||||||| ||||||||||| || ||  |||| |||| ||| || |||||||||||| | |||||||||||  | |||| | | | |  |||            |||   || |||   | |||     |  ||  || ||| | | | |   |   |                   
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgattttggttttaagcttcacctggat

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT5G66140.1 (Arabidopsis thaliana), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttc-gtttccctctgatctctagacctctagatttctagctcctgattccgaaatctctgtccag------------------------------------
| ||||| || ||||| |||||||||||||| |||||||| || |||||  | || |||| ||| |||||||| |||||| ||||||| |||||  | |||||   ||||| |||  || ||       | |    | |  |         |   |||||    |                                     
AAGCCGTCCGCAAGGGTAACGCCGCCGTCGGTGTCCGCGGTACCGACACCGTTGTCCTCGCCGTCGAGAAGAAGTCCACCCCCAAGCTTCAGGATTCTAGgttttatttccatctcttcacttttatcatgg--caccaattaacagacttgccctctctacttattggatcctgcttggtttactctcagttgctagttga

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttccctct------gatctctagacctctagatttctagctcctgattccgaaatctctgtccag-----------------------------
| ||||| || |||||||||||||||||||||||||||||||| ||||| ||||| |||||||| || ||||| |||||||| |||||||||||| |  ||| | | ||   ||      |||  |      ||     || | | |   |||   ||| |||  |||                                
AAGCCGTCCGTAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTCCTCGGCGTCGAAAAGAAGTCCACCGCTAAGCTCCAGGACTCTCGgtacctctcttcctctctacgattacgcattttcagtgattgtggtttaagatcgtgaattctgagtcagcttttgaacctatctgatggtttctgtggc

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttccctctgatctctagacctctagatttctagctcctg---attccgaaatctctgtccag--------------------------------
| ||||| || || ||||||||||||||||||||||||||||| ||||| ||||| |||||||| ||||| || ||||||||||| ||||| ||  | ||||    ||   ||   | ||        |   ||| |  ||  ||   || || ||||    ||   |                                
AAGCCGTCCGTAAAGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTTCTCGGCGTCGAGAAAAAGTCCACCGCCAAACTCCAAGATTCCAGgtctccttttttcatttttcatttttattttctttttttcttgtgtaaataccaaaatgaaggtagggttagggtttgatggttttggagacatccatgt

upper sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S12_77V6.1 (Physcomitrella patens), 5'ss of exon 1
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-tcgtttccctctgatctctagacctctagatttctagctcctgattccgaaatctctgtccag-----------------------------------
| || ||| ||||||| || || || ||||| || || ||||||||||| || ||| | ||||||||||||||||||||  | ||| | || || ||  ||| | | |   ||   |||      |   |    ||   |||  ||| | |       | ||  ||                                   
AAGCTGTGAGAAAGGGAAATGCAGCAGTCGGGGTGCGAGGCACTGACACCATTGTGTTGGGCGTGGAGAAGAAATCCACTACTAAGTTGCAAGATGCCCGgtattgctcttcttctatcctgctgcagttgttattgatgcttgtgaatgccttggtgc-gtttaggtgatcaatcttaggtgtgaagggtgcatttaggt

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|169053862|gb|FE460953.1|FE460953
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTCCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169067023|gb|FE474440.1|FE474440
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169073950|gb|FE483430.1|FE483430
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTCCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169067024|gb|FE474441.1|FE474441
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169051265|gb|FE457615.1|FE457615
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169092978|gb|FE495272.1|FE495272
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169092979|gb|FE495273.1|FE495273
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169051264|gb|FE457614.1|FE457614
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169049284|gb|FE459560.1|FE459560
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTCCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169053861|gb|FE460952.1|FE460952
EST:     GAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTCCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: GAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169040197|gb|FE448119.1|FE448119
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169073951|gb|FE483431.1|FE483431
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTCCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
EST: gi|169071075|gb|FE480703.1|FE480703
EST:     ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAG                         GACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC
genomic: ATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGC

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), 22 (downstream exon)
Score: 14

AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttcc ... ctctgtccagGACGGTGCACAAGATCCTGAGCCTCGACGAGCACGTCGCCCTAGCTTTCGCTGGCCTCACAGCCGACGCCAGGGTCCTGGTGAACCGGGCGAGAGTGGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgttcgtttccctctgatctctagacctctagatttctagctcctgattccgaaatctctgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT