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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcatttgcccag

Basic information

species Selaginella moellendorffii
transcript EFJ30452
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G132968_T02 (Zea mays), 5'ss of exon 3
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctg--ttcttcccatttcgagagctaaatt--tcgc---gttcatttgcccag--------------------------------------
||  ||||||| || | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |    |||||     ||    |  ||| ||  || |   || || ||                                            
CCCAGGGATGACCCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagttgatcacatagtccagttttttgatatctgaaaaatgaactgtaacaacacaactatttctt

upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G109677_T03 (Zea mays), 5'ss of exon 5
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcat-ttgcccag----------------------------------------------
||| ||||||| || | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |    | | |  ||| |  |   || |     | | |  | | ||||                                              
CCTAGGGATGACCCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacc--cccttcgtttttgttaatcaattaagctgatgacatagtccagtttgtttatatctgaaaaatgaattgtaacataagcatgatttgat

upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM5G801409_T04 (Zea mays), 5'ss of exon 2
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctg---ttcttcccatt--tcga--gagctaaatttcgcgttca-tttgcccag-------------------------------------
||| |||||||  | | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |     |  ||   |||  || |   |||| |       || || ||||   |                                      
CCTAGGGATGACGCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagctgaggacatagtccagtttgtttatatctgaaaaatgaattgtaacataagaacgatttgat

upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G324314_T05 (Zea mays), 5'ss of exon 3
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcat-ttgcccag----------------------------------------------
||| ||||||| || | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |    | | |  |||    |   || |     | | |  | | ||||                                              
CCTAGGGATGACCCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacc--cccttcttttttattaatcaattaagctgatgacatagtccagtttgtttatatctgaaaaatgaattgtaacatgagaacgatttgat

upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM2G135727_T03 (Zea mays), 5'ss of exon 3
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctg--ttcttcccatttcgagagctaaatt--tcgc---gttcatttgcccag--------------------------------------
||  ||||||| || | ||||     |||| | || |||||| | || |||||||| ||||||||||| || ||||| ||||| |||||||||||||| |||| |||| |    |||||     ||    |  ||| ||  || |   || || ||                                            
CCCAGGGATGACCCCAAGAAGCCTTGCCATCTCACTGCCTTCCTTGGCTACAAGGCTGGCATGACTCACATTGTCCGTGAGGTTGAGAAGCCAGGATCCAgtatgtccacccccttcttttttattaatcaattaagttgatcacatagtccagttttttgatatctgaaaaatgaattgtaacataagcacgatttgat

upper sequence: EFJ30452 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA10G36780.1 (Glycine max), 5'ss of exon 3
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctgttcttcccattt-cgagagctaaatttcgcgt--tcatttgcccag------------------------------------------
||   |||||| ||  | |||   ||| |  | || || ||| |||| ||||||||||| |||||||| || ||  | |||||||||||||||||||| ||| ||| |  |  | | |  |||      || |||||         || |   ||  |                                          
CCCAAGGATGACCCATCCAAGGCACCCAAGCTCACTGCATTCTTGGGTTACAAGGCCGGTATGACTCACATTGTTAGAGAGGTCGAGAAGCCAGGATCAAgtgagttccatactttgctaattaattgaagttaaatgatataatgtcgtcaaccatgtgttttactcagctacttacttgatcaccaatagcaggactg

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|70671032|gb|DN839609.1|DN839609
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169062675|gb|FE470345.1|FE470345
EST:     CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169099960|gb|FE503448.1|FE503448
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|70670339|gb|DN838916.1|DN838916
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169074641|gb|FE481196.1|FE481196
EST:     CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169036555|gb|FE444126.1|FE444126
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169054887|gb|FE463491.1|FE463491
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
EST: gi|169063852|gb|FE471207.1|FE471207
EST:     CAAGGCCGGTATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTA                         AGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC
genomic: CAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCAC

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: 85

CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgc ... atttgcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCACCGCTCATTATCGTCGGAGTGGTGGCGTACATTAAGACTCCTCGCGGCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAAGCCAGGATCTAgtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcatttgcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC