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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagagagaaaattttcttcgattcttttgatttcgtgctgcttagaaatctttgcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ33020
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 5'ss of exon 1
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaaggga--agagagaaaattttcttcgattcttttgatttcgtgc---tgcttagaaatctttgcgcag-----------------------------
|| || | ||||||    ||||||||   ||| ||||||||||| ||||||||||| |||||||| || || |||||||||||||||||||| ||||| ||||| |    |    |   |      ||  | ||  || |  || |    || |      || | ||                                 
GCGGCGGAGATGAACGCGTTCCGGCTAGCCGGGGACATGACCCACCTCCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGgtaacgcgccacgccgcggacccaaatctttgctgctgctgccgcgtgtatgatccactctcctcgcctgttcggcagctattctgctttacttttcttt

upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os11g28340.2 (Oryza sativa), 5'ss of exon 1
-------------------GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCAC--ACCATCAAGTCTTG-CGCCGgtaagggaagagagaaaattt--tcttcgattcttttgatttcgtgctgcttagaaatctttgcgcag----------
                           |||  | | | ||  |  |||||  |  |   | |  | || | |   |       |||||||   |   |    |  ||| | |||   |||| ||  || |          |||  | |||  |  | ||   ||||   |   ||| |   | |||||            
CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatccactctcctcgcctgttcggcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt

upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os04g30800.2 (Oryza sativa), 5'ss of exon 1
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagag--agaaaatt------ttctt------cgattcttttgatttcgtgctgcttagaaatctttgc--gcag------------------
|| |  | ||||||   |||| |||||  ||| |||||||| ||  || | |||||| | || || |||||||||||||||||||||||||||||||| ||| || ||      ||   | |      | |||      |  || |||| | |   |   |    | | |  ||||  ||||                  
GCGGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt

upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os04g30800.1 (Oryza sativa), 5'ss of exon 1
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagag--agaaaatt------ttctt------cgattcttttgatttcgtgctgcttagaaatctttgc--gcag------------------
   |  | ||||||   |||| |||||  ||| |||||||| ||  || | |||||| | || || |||||||||||||||||||||||||||||||| ||| || ||      ||   | |      | |||      |  || |||| | |   |   |    | | |  ||||  ||||                  
--GGGCGAGATGAACGCCTTCAGGCTCGCCGGGGACATGACGCACATCATGAGCGTCCTCGTCCTCCTGCTCAAGATCCACACCATCAAGTCTTGCGCTGgtgagtgactgatcagccgactggcgcctgcttaagatgcatttttttttactgtattgagtcctggattggttgccagcagctcaagaaaggtagagtt

upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagagagaaaattttcttcgattcttttgatttcgtgctg----cttagaaatct-------ttgcgcag-------------------------
| | | | ||||||  | ||||||||    || ||||||||||| ||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| |||| |                ||| ||   |  | |  |  | |||       ||| || |        |||||| |                         
GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgtacgcccttctcttc--ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg

upper sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G46570.1 (Glycine max), 5'ss of exon 1
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag--------agagaaaattttcttcgattcttttgatttcgtgctgcttagaaatctttgcgcag---------------------------
  || |  ||||||||| ||| || |   ||| |||||||||||| |   ||||||| | || || || |||||||||||||||||||| || |||||||||  |             |     ||  ||| ||| |   | || ||| ||   | | || |    | |   |                            
TAAGAAAAGATGAATATTTTCAGGTTAGCCGGGGACATGACCCATTTGGCCAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtaccttcctttccaatctcaacattcatcgctcgctctg-ttttgtttcgttgaggatatgtcgtagattttcattgtaataatgctgacgtgtgt

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|169112068|gb|FE510720.1|FE510720
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169059929|gb|FE467291.1|FE467291
EST:     CTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169046459|gb|FE454746.1|FE454746
EST:     CGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTNTGCGACGCGCT
genomic: CGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169111123|gb|FE509372.1|FE509372
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169036709|gb|FE444930.1|FE444930
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169051950|gb|FE460081.1|FE460081
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169112069|gb|FE510721.1|FE510721
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169053109|gb|FE463008.1|FE463008
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169046473|gb|FE454747.1|FE454747
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169064230|gb|FE471585.1|FE471585
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169059930|gb|FE467292.1|FE467292
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169103529|gb|FE507597.1|FE507597
EST:     CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
genomic: CAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT
EST: gi|169053108|gb|FE463007.1|FE463007
EST:     TGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCG                         GGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTNTGCGACGCGCT
genomic: TGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCT

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), 34 (downstream exon)
Score: 17

GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaag ... ctttgcgcagGGATTTCTCTCAAGACGCAGGAGCTCTATGCCCTCGTCTTTGCGACGCGCTACTTGGATATTTTCACGCACCATGTCTCGCTCTATAACACGGTGATGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCACACCATCAAGTCTTGCGCCGgtaagggaagagagaaaattttcttcgattcttttgatttcgtgctgcttagaaatctttgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT