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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag

Basic information

species Selaginella moellendorffii
transcript EFJ06181
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 4
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatca-tttgatttgt--------cctctgatatt--gtttttgcttctcag---------------
||||||||||||||| ||||||||||||| || || |||||  | || || ||||| |||||||| |||||| | |||||  |  | |     |  |  | | |  |||||        |   | | ||   ||  |||  | |                  
ACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAAgtatactatacaacaacacaaatctagtttgtgtaaataacaatttacatccagtgattgtattttgnatatttttgttgtag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G427097_T01 (Zea mays), 5'ss of exon 4
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag------------------------------------------------------------------
|||||||| ||||| |||||||||||||| || ||||||||  |||| |||||||| |||||||| |||||| | ||||| |       | |       | || | |||    |    |   ||||| |     |                                                                   
ACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAgtaag-tgaaaaaatgtggcagcaagttaaattggtgccaataaacttttttacaaagtataatataacagaaaaaatgtacacaatagttattatcatttttactcttttttgtttgttgttgtag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA02G07940.1 (Glycine max), 5'ss of exon 5
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgta--------agcttgttt---ttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag----------------------------
|| ||||| |||||||| |||||||| ||||| ||||||||  |||||||||||||||| ||||| || ||  | |||        |   |||||   ||| | ||  | ||  |  |||  || ||  |         ||| |||                             
ACTATGGCATGGATTCTAGATGAGTATTCCAAATTTCATGGCCACTCTCCAGCAGTAGTGACTGGGAAACCTATAgtacgtagattaaactgtttgtatttctcattttaatgagcattgaactgtgccacaacagcaacttatcaacacactctttctacgattggattattag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA01G41310.1 (Glycine max), 5'ss of exon 4
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag---------------------------------------
|| |||||||||||||| |||||||| || |||||||||||  | || |||||||| || ||||| || ||  | |||||  |  | |   | || ||| |||| | |    |     ||  |   |  ||   ||                                       
ACAATGGCTTGGATTCTTGATGAGTATTCTAAGTTTCATGGACATTCACCAGCAGTTGTGACTGGGAAACCTATAgtaagtataatgtgcataatcatcctttgttcttgtatacacaatcataacttatttgtagaaattgttttaattttcaacattttttgttgtggtgtag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA05G05460.1 (Glycine max), 5'ss of exon 4
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagctt---gtttttttttatgatcatttgattt----gtcctctgatattgtttttgcttctcag----------------------------------
|||||||| |||||||| |||||||| || |||||||||||| | || || ||||| || || || |||||  |||||||  |    |       || | | |   || |      || |||| |  ||| | |     | |                                   
ACCATGGCATGGATTCTCGATGAGTATTCAAAGTTTCATGGGCATTCACCTGCAGTTGTGACAGGGAAGCCTATTgtaagtatcaaatacacacatacgcttaagagactgcaaaatcttctgttgatgtgtatatcaatgattaggaaattgtctttgaatgtttttttcctgcag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT5G07440.1 (Arabidopsis thaliana), 5'ss of exon 3
-------------------------ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatcatttgatt-tgtcctctgatattgtttttgcttctcag--------------------------------------------------------------------------------------------------
                         ||||||||||||||||| |||||||||||||||||||||||  | || || || || ||||||||||||||  |||||||  | ||    ||| || | || | ||| ||    | ||   |||| ||  ||||  |                                                                                                  
TCCTGATATGGGCACTAACGCTCAAACCATGGCTTGGATTCTTGATGAGTACTCCAAGTTTCATGGTCATTCCCCTGCTGTTGTCACTGGAAAGCCCATTgtaaggcttttaagattt-tggttatatcattctgagtccggaatctgttgtttattctatggatgttttcttgatttgaattaattcgatgtttctatgtgattaccatagttttgagctttttggtatagaagtaactgttggatcactttggtgtag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 5'ss of exon 4
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagc------------ttgtttttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag-------
|| |||||||||||||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||  |||||||                | || ||||   |     || |||  || |    ||  ||  || |  | |        
ACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATTgtaagtaaagaataatcacaatcttgttttgctaatgactggtttaaccacctgaatgtttaatgatgtttatgaaccag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv00s1491g00010.t01 (Vitis vinifera), 5'ss of exon 2
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagctt----------------gtttttttttatgatcatttgatttg----------tcctctgatattgtttttgcttctcag
|| ||||| |||||||||||||| ||||| |||||||||||| | || || ||||| || || ||||||||| |||||||  |                     |  | |  ||  || || |||          ||| |  | ||| || | || | | ||
ACGATGGCATGGATTCTGGATGAATACTCAAAGTTTCATGGGCATTCACCTGCAGTTGTTACAGGAAAGCCAATTgtaagtatcaaggagggagaggaaaccagtggtcaatatacttcgaattgaaggccaatgtccacccaaattattct-gcattttag

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 5'ss of exon 6
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtt-tttttttatgatcatttga----------tttgtcctctgatattgtttttgcttctcag----------------------------
|||||||| ||||| || ||||||||||| || |||||||| ||||| || || || || |||||||||||  |||| ||  | |     | |||||||   ||||          ||| | |  | ||  |   |||| ||  | |                            
ACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATTgtgagtatatagcactcttatgatgggttgaaaagtacaggtttataccataattgtaggtttgatttcctgtagatgtaaatttctgctgattcaagta

upper sequence: EFJ06181 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgtttttttttatgatcatttgatttgtcctctgatattgtttttgcttctcag------------------------------------------------
|| |||||||||||| |||| |||||||| || |||||||||||  |||| || || || ||||| || ||  | ||||| |  | | |  |    |  | |   |    | |      |||||      | | |                                                 
ACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTGgtaagttaatgtctcctaccaaaaactgtgtacagcttaaccgcttgttcagatgtttgaatgactatccctttcctacgattgatccttttcttttactttcatgaag

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|169046220|gb|FE456379.1|FE456379
EST:     ACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACT-GAAAGCCACTT                         GACCTAGGTGGCTCTGTAGGACGTGAGGCTGCCACTGGAAGAGGAGTGGTA
genomic: ACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgt ... tgcttctcagGACCTAGGTGGCTCTGTAGGACGTGAGGCTGCCACTGGAAGAGGAGTTGTA
EST: gi|169067884|gb|FE474755.1|FE474755
EST:     ACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTT                         GACCTAGGTGGCTCTGTAGGACGTGAGGCTGCCACTGGAAGAGGAGTTGTA
genomic: ACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgt ... tgcttctcagGACCTAGGTGGCTCTGTAGGACGTGAGGCTGCCACTGGAAGAGGAGTTGTA

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: 51

ACCATGGCTTGGATTCTGGATGAGTACTCCAAGTTTCATGGGTACTCTCCAGCAGTAGTCACTGGAAAGCCACTTgtaagcttgt ... tgcttctcagGACCTAGGTGGCTCTGTAGGACGTGAGGCTGCCACTGGAAGAGGAGTTGTATACGTGACTGAAGCATTGCTTGCCGACCATGGCAAGTCTCTCTCGAACC




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