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1  
 5'  3'   
2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatcaaaaaccatctttttcttcgatatctccattgattggtttgtttttctttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ26016
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os11g06890.1 (Oryza sativa), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgat-cgatcaaaaaccatctttttcttcgata-tctccattgattggt-ttgtttttctttgcag---------------------------
| || || |||||||| ||||| ||||||||||| || || |||||||| |||||| | || |||||||| ||||| || |||||||| ||||| ||| ||||| | | | | |||| | | | || | | || || | || | | | ||| |
TCTTTGACGGCTACGCGCATCTGTCGTCCGGGCTCGCCTGTGGCCTCGCCGGTCTCGCTGCCGGAATGGCCATCGGCATCGTCGGTGATGCTGGTGTCAGgtaaagatgctgcctgctttgttgatctgtgatgtagttagtgtgtatatgctgttactgctgtgcattggtgattaagtatggttttatgatggaagct

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AC216067.3_FGT002 (Zea mays), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaa-gttcgatcgatc-----aaaaaccatctt-tttcttcgatatctccattgattggtttgtttttctttgcag-----------------------
| || |||||||||||||| || ||||||||||| || || ||||| || || || | ||||| ||||| ||||| ||||| ||||| ||||||||| ||||| | || || || | |||| | | | | | || || | | | | ||| |||
TTTTTGATGGCTACGCTCACCTTTCGTCCGGGCTTGCCTGTGGCCTTGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctccctctctctttgtagtggacatcatatatttactatgtccttttcctactatctactattcaatgccatggccagaatgttgatattgtgc

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G177005_T01 (Zea mays), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaa---gttcgatcgatcaaaaaccatctttttcttcgatatctccattgattg--gtttgtttttctttgcag---------------------------
| || ||||||||||| || || ||||||||||| || || || ||||| || || | ||||| ||||| ||||| ||||||||||| ||||||||| ||||| | || || | | | |||| | || ||| ||| || ||| || || | | | |||
TCTTTGATGGCTACGCCCACCTTTCGTCCGGGCTTGCCTGTGGTCTCGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTCGGTGATGCTGGAGTCAGgtaaaaggctctctctgt-agtgagcatcatagattt-actatgtccttttattactgtctgctatgccatgccatgcccagaatgttaatattgtgttatt

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA11G07980.1 (Glycine max), 5'ss of exon 1
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatcaaaaaccatctttttcttcg-----atatctccattgattggtttgtttttctttgcag-------------------------
| ||||| ||||||||||| || || ||||| || |||||||||||||| || ||||| ||||| ||||| || || ||||| || || || || || |||| || || | | |||||||||| ||| | || || | || | | || |
TCTTCGACGGCTACGCTCACCTCTCCTCCGGCCTCGCTTGCGGCCTCGCTGGCCTCTCCGCTGGCATGGCCATTGGCATTGTTGGCGATGCCGGTGTTAGgtattctcactcattttctatttttctttttctttttacttataacatgatcgaataagatgcgtatagttataattattttcttgcgtatggttaggta

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA14G23990.1 (Glycine max), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatc--aaaaaccatctttttcttcgatatctccattga--ttggtttgtttttctttgcag--------------------------
| || |||||||| || || | || || || || || || |||||||| || ||||| ||||||||||| || |||||||| ||||| ||||| ||| ||||| | || || | | ||| | | ||| | || || | || | || || ||
TCTTTGATGGCTATGCCCACTTGTCCTCTGGCCTCGCCTGTGGCCTCGCTGGCCTCTCTGCTGGAATGGCCATTGGGATTGTTGGTGATGCTGGTGTCAGgtaattgttattcattttcattatcatgatcatgccatgtatgcctatggacacttcttgaatgttaggtgtagtaagtgttggagatctttatattgat

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatcaaaaaccatcttt-ttcttcgatatctcca---ttgattggtttgtttttctttgcag--------------------------
| ||||||||||| |||||||| || || ||||| ||||| || || || |||||||| ||||| ||||| || || || |||||||| ||||| || ||||| | | ||| | | | ||||| | || ||| | || ||||| | ||| || ||| |
TATTCGATGGCTATGCTCATCTCTCTTCTGGGCTAGCTTGTGGTCTTGCTGGTCTCTCTGCTGGTATGGCTATTGGAATCGTCGGTGATGCTGGTGTTAGgtaattgctatctctgctacatgatcttaactgtttgattgcagcaattttgatcgattttcacttgtttagaagtttctgagatagctttgttgtttgt

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT4G34720.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttc--gatcgatcaaaaaccatctttttcttcgatatctccattgat-tggtttgtttttctttgcag------------------------
| || ||||| ||||| ||||| ||||| || || ||||| || || || |||||||| ||||||||||| || |||||||| ||||| || || ||| ||| || || | || | | | ||| ||| || || | ||||
TCTTTGATGGATACGCACATCTCTCGTCTGGTCTTGCTTGTGGTCTTGCTGGTCTCTCAGCTGGAATGGCCATTGGGATTGTTGGTGATGCCGGTGTCAGgtttgtctctcgtcctcctgctactgatacgctttgaggtattatggaagatatgtaacattggtgtttgacttacccttttgcgattctttttcag

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatcaaaaaccatctttttcttcgatatctccattgattggtttgtttttctttgcag----------------------------------
| ||||||||||| |||||||| || ||||| || ||||| || ||||| |||||||| || || ||||| || || |||||||| || || || || ||||| | ||||| ||| | ||| | | | ||| | ||| | | | | | | || | |
TATTCGATGGCTATGCTCATCTCTCTTCCGGTCTTGCTTGTGGTCTCGCTGGTCTCTCCGCCGGTATGGCTATTGGAATTGTCGGCGATGCCGGTGTTAGgtaattc---tcgattaaatttc-tctatatgatgtataacctaattcaattggtcgaatacgttggaaacttttcagaaaatatcttaggcttggtttgattc

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga-------tcgatcaaaaaccatctttttcttcgatatctc-cattgattggtttgtttttctttgcag----------------------
| || ||||| ||||| || || || || || ||||||||||||||||| || || || ||||||||||| || ||||| |||||||| ||||| || |||| || | ||| | || || | | | | | |||| ||| || | || |
TTTTTGATGGTTACGCACACCTTTCTTCTGGTCTGGCTTGCGGCCTCGCTGGCCTTTCTGCTGGAATGGCCATTGGGATAGTCGGTGATGCTGGTGTGAGgtatattgctctctgccttgattctgatttataaggttgcttaacaacgctcatttgttgtgccattgtgaatttgggttatactatatttgcattttgt

upper sequence: EFJ26016 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 5'ss of exon 2
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcg---atcgatcaaaaaccatctttttcttcgatatctccattgattggtttgtttttctttgcag----------------------------
| ||||||||||| || ||||| ||||| || |||| || || || || || |||||||| |||||||||||||||||||| || || || || ||| ||||| | | | ||| | | |||| | | | | | || || |||| | || || |
TTTTCGATGGCTATGCGCATCTCTCGTCGGGTTTGGCGTGTGGTCTGGCCGGGCTCTCGGCCGGAATGGCAATCGGGATTGTTGGCGATGCCGGTGTCAGgtaattgcataatttgatttagatgttgagttttgatgggtggtttcgtttgatg-tttgatattgttaacgcgcctgtgacattacatgaagaatatggt

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|169045837|gb|FE453071.1|FE453071
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169026566|gb|FE434814.1|FE434814
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169049088|gb|FE457076.1|FE457076
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169041312|gb|FE446855.1|FE446855
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169087043|gb|FE496188.1|FE496188
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169112705|gb|FE515081.1|FE515081
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169110062|gb|FE511574.1|FE511574
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169087044|gb|FE496189.1|FE496189
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169066184|gb|FE475684.1|FE475684
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169049954|gb|FE458046.1|FE458046
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169095914|gb|FE499957.1|FE499957
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169095950|gb|FE497302.1|FE497302
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169036530|gb|FE444114.1|FE444114
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169041326|gb|FE446856.1|FE446856
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169024664|gb|FE432834.1|FE432834
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169049955|gb|FE458047.1|FE458047
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169057068|gb|FE466295.1|FE466295
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
EST: gi|169074126|gb|FE481864.1|FE481864
EST:     GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCG                         GGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT
genomic: GGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCAT

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: 91

TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcga ... ttctttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCGATGGCTACGCTCATCTATCGTCCGGGCTGGCTTGCGGCCTCGCGGGTCTCTCGGCTGGAATGGCAATCGGGATTGTCGGTGACGCTGGAGTCCGgtaagttcgatcgatcaaaaaccatctttttcttcgatatctccattgattggtttgtttttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA